Merge pull request #1 from monarch-initiative/trim

Update this repo to be TALISMAN only

README.md

@@ -1,88 +1,21 @@
-# OntoGPT
-
-[![DOI](https://zenodo.org/badge/13996/monarch-initiative/ontogpt.svg)](https://zenodo.org/badge/latestdoi/13996/monarch-initiative/ontogpt)
-![PyPI](https://img.shields.io/pypi/v/ontogpt)
+# TALISMAN
 
 ## Introduction
 
-_OntoGPT_ is a Python package for extracting structured information from text with large language models (LLMs), _instruction prompts_, and ontology-based grounding.
+_TALISMAN_ is a Python package for summarizing gene set functions using large language models (LLMs).
 
-Two different strategies for knowledge extraction are currently implemented in OntoGPT:
+It uses the OntoGPT package to interface with LLMs.
 
-[For more details, please see the full documentation.](https://monarch-initiative.github.io/ontogpt/)
+[For more details, please see the full documentation.](https://monarch-initiative.github.io/talisman/)
 
 ## Quick Start
 
-OntoGPT runs on the command line, though there's also a minimal web app interface (see `Web Application` section below).
-
-1. Ensure you have Python 3.9 or greater installed.
-2. Install with `pip`:
-
-    ```bash
-    pip install ontogpt
-    ```
-
-3. Set your OpenAI API key:
-
-    ```bash
-    runoak set-apikey -e openai <your openai api key>
-    ```
-
-4. See the list of all OntoGPT commands:
-
-    ```bash
-    ontogpt --help
-    ```
-
-5. Try a simple example of information extraction:
-
-    ```bash
-    echo "One treatment for high blood pressure is carvedilol." > example.txt
-    ontogpt extract -i example.txt -t drug
-    ```
-
-    OntoGPT will retrieve the necessary ontologies and output results to the command line. Your output will provide all extracted objects under the heading `extracted_object`.
-
-## Web Application
-
-There is a bare bones web application for running OntoGPT and viewing results.
-
-First, install the required dependencies with `pip` by running the following command:
-
-```bash
-pip install ontogpt[web]
-```
-
-Then run this command to start the web application:
-
-```bash
-web-ontogpt
-```
-
-NOTE: We do not recommend hosting this webapp publicly without authentication.
-
-## Evaluations
-
-OpenAI's functions have been evaluated on test data. Please see the full documentation for details on these evaluations and how to reproduce them.
-
-## Tutorials and Presentations
-
-- Presentation: "Staying grounded: assembling structured biological knowledge with help from large language models" - presented by Harry Caufield as part of the AgBioData Consortium webinar series (September 2023)
-  - [Slides](https://docs.google.com/presentation/d/1rMQVWaMju-ucYFif5nx4Xv3bNX2SVI_w89iBIT1bkV4/edit?usp=sharing)
-  - [Video](https://www.youtube.com/watch?v=z38lI6WyBsY)
-- Presentation: "Transforming unstructured biomedical texts with large language models" - presented by Harry Caufield as part of the BOSC track at ISMB/ECCB 2023 (July 2023)
-  - [Slides](https://docs.google.com/presentation/d/1LsOTKi-rXYczL9vUTHB1NDkaEqdA9u3ZFC5ANa0x1VU/edit?usp=sharing)
-  - [Video](https://www.youtube.com/watch?v=a34Yjz5xPp4)
-- Presentation: "OntoGPT: A framework for working with ontologies and large language models" - talk by Chris Mungall at Joint Food Ontology Workgroup (May 2023)
-  - [Slides](https://docs.google.com/presentation/d/1CosJJe8SqwyALyx85GWkw9eOT43B4HwDlAY2CmkmJgU/edit)
-  - [Video](https://www.youtube.com/watch?v=rt3wobA9hEs&t=1955s)
+TBD
 
 ## Citation
 
-The information extraction approach used in OntoGPT, SPIRES, is described further in: Caufield JH, Hegde H, Emonet V, Harris NL, Joachimiak MP, Matentzoglu N, et al. Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. arXiv publication: <http://arxiv.org/abs/2304.02711>
-
-The gene summarization approach used in OntoGPT, SPINDOCTOR, is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: <http://arxiv.org/abs/2305.13338>
+The gene summarization approach used in TALISMAN is described further in: Joachimiak MP, Caufield JH, Harris NL, Kim H, Mungall CJ. Gene Set Summarization using Large Language Models. arXiv publication: <http://arxiv.org/abs/2305.13338>
 
 ## Acknowledgements
 
-This project is part of the [Monarch Initiative](https://monarchinitiative.org/). We also gratefully acknowledge [Bosch Research](https://www.bosch.com/research) for their support of this research project.
+This project is part of the [Monarch Initiative](https://monarchinitiative.org/).