diff --git a/tests/integration/test_cli/test_cli.py b/tests/integration/test_cli/test_cli.py index ffa52a908..c98e17805 100644 --- a/tests/integration/test_cli/test_cli.py +++ b/tests/integration/test_cli/test_cli.py @@ -1,12 +1,10 @@ """Tests the command-line interface.""" import unittest -import inflection from click.testing import CliRunner -import tests.integration.test_knowledge_engines.test_cases as extract_cases from talisman.cli import main -from tests import CASES_DIR, OUTPUT_DIR +from tests import OUTPUT_DIR from tests.integration.test_knowledge_engines.test_enrichment import PEX CACHE_DB = str(OUTPUT_DIR / "cli_cache.db") @@ -27,86 +25,6 @@ def test_main_help(self): self.assertIn("halo", out) self.assertEqual(0, result.exit_code) - def test_extract(self): - for case in extract_cases.CASES: - template, input_name = case - input_file = str(CASES_DIR / f"{input_name}.txt") - fmts = ["yaml", "html", "md"] - if template == "recipe": - fmts.append("owl") - for fmt in fmts: - output_file = str(CLI_OUTPUT_DIR / f"{input_name}.{fmt}") - cmd = [ - "--cache-db", - CACHE_DB, - "extract", - "-t", - template, - input_file, - "-O", - fmt, - "-o", - output_file, - ] - print(cmd) - result = self.runner.invoke(main, cmd) - self.assertEqual(0, result.exit_code) - out = result.stdout - print(out) - - def test_pubmed_extract(self): - cases = [ - ("PMID:32044947", "treatment.DiseaseTreatmentSummary"), - ] - for pmid, template in cases: - for fmt in ["yaml", "html"]: - output_file = str(CLI_OUTPUT_DIR / f"pmid-{pmid}-{template}.{fmt}") - cmd = [ - "--cache-db", - CACHE_DB, - "pubmed-extract", - "-t", - template, - pmid, - "-O", - fmt, - "-o", - output_file, - ] - print(cmd) - result = self.runner.invoke(main, cmd) - self.assertEqual(0, result.exit_code) - out = result.stdout - print(out) - - def test_search_and_extract(self): - cases = [ - ("treatment.DiseaseTreatmentSummary", "COVID-19", ["review"]), - ] - for template, term, keywords in cases: - for fmt in ["yaml", "html"]: - safe_term = inflection.underscore(term) - output_file = str(CLI_OUTPUT_DIR / f"{template}-search-{safe_term}.{fmt}") - cmd = [ - "--cache-db", - CACHE_DB, - "search-and-extract", - "-t", - template, - term, - "-O", - fmt, - "-o", - output_file, - ] - for kw in keywords: - cmd.extend(["-k", kw]) - print(cmd) - result = self.runner.invoke(main, cmd) - self.assertEqual(0, result.exit_code) - out = result.stdout - print(out) - def test_enrichment(self): ids = [id for id, _ in PEX] cmd = ["enrichment"] + ids diff --git a/tests/integration/test_clients/__init__.py b/tests/integration/test_clients/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/integration/test_clients/test_openai_client.py b/tests/integration/test_clients/test_openai_client.py deleted file mode 100644 index 227d31d42..000000000 --- a/tests/integration/test_clients/test_openai_client.py +++ /dev/null @@ -1,222 +0,0 @@ -"""Open AI client tests.""" -import re -import unittest - -import yaml - -from talisman.clients.openai_client import OpenAIClient -from tests import PROMPTS_FILE - -PROMPT = """ -example: - -name: ornithine biosynthesis -def: The biological process that results in the output of ornithine, ornithine, - an amino acid only rarely found in proteins, but which is important in living - organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. -parent: biosynthetic process -differentia: - outputs: ornithine - -=== - -name: selenocysteine biosynthesis -""" - -CODE_PROMPT_GENERALIZATION = """ -- name: ornithine biosynthesis - description: The biological process that results in the output of ornithine, - ornithine, an amino acid only rarely found in proteins, but which is important in - living organisms as an intermediate in the reactions of the urea - cycle and in arginine biosynthesis - subclass_of: - - amino acid biosynthetic process - pattern: - - biosynthetic process - outputs: - - ornithine -- name: selenocysteine biosynthesis -""" - -CODE_PROMPT_EXTRACT = """ -- abstract: >- - Amelogenesis imperfecta type 1K (AI1K) is characterized by hypoplastic enamel of all teeth. - In some individuals, the pulp chambers may be enlarged and some molars may exhibit taurodontism - Amelogenesis imperfecta segregated as an autosomal dominant trait in the family described by - Smith et al. - amelogenesis imperfecta type IK (AI1K) is caused by heterozygous mutation in the - SP6 gene (608613) on chromosome 17q21. - - name: amelogenesis imperfecta type 1K - synonyms: - - AI1K - subclass_of: - - amelogenesis imperfecta - genes: - - SP6 - inheritance: autosomal dominant - phenotypes: - - hypoplastic enamel - - pulp chamber enlargement - - taurodontism -- abstract: >- - Familial hemiplegic migraine-2 (FHM-2) is a rare subtype of familial hemiplegic migraine (FHM) - characterized by migraine with aura, - nystagmus, and progressive cognitive decline. It is caused by mutations in ATP1A2. - name: Familial hemiplegic migraine-2 - synonyms: - - FHM2 - - Familial hemiplegic migraine type 2 - subclass_of: - - familial hemiplegic migraine - genes: - - ATP1A2 - inheritance: autosomal dominant - phenotypes: - - migraine with aura - - nystagmus - - progressive cognitive impairment -- abstract: >- - neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) - is caused by heterozygous mutation in the FRMD5 gene. - Neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) - is characterized by global developmental delay apparent from infancy. - Affected individuals show delayed walking with an unsteady gait, - variably impaired intellectual development, learning disabilities, - and speech difficulties. Abnormal eye movements, which are often noted in early childhood, - include opsoclonus, nystagmus, and strabismus. Some patients have seizures, - which may be refractor. - Lu et al. (2022) reported 8 unrelated patients, ranging in age from 3 to 27 years, - with a similar neurodevelopmental disorder and de novo heterozygous mutations - in the FRMD5 gene. The patients presented in infancy with global developmental - delay and showed delayed walking, variably impaired intellectual development, - and poor or absent speech. Those that achieved walking had an unsteady gait, - and most had hypotonia and ataxia; a few demonstrated spasticity. - Some patients had dyslexia or learning disabilities. Six patients had seizures - or evidence of seizures, including 2 patients who were diagnosed in infancy - with refractory epilepsy and West syndrome. All patients had eye movement abnormalities, - ranging from strabismus and intermittent esotropia to opsoclonus and nystagmus. - Two were visually impaired and had myopia or hypermetropia. Brain imaging was normal - in most patients, but one had pachygyria and another had delayed myelination. - A few patients had additional features such as myoclonus, dystonia, dyskinesia, - and behavioral problems. - Inheritance: - The heterozygous mutations in the FRMD5 gene that were identified in most - patients with NEDEMA by Lu et al. (2022) occurred de novo. - - name: """ - -TUNED_TEST_PROMPT = """ -From the text below, extract the following entities in the following YAML:: - -name: -synonyms: -subclass_of: -genes: -inheritance: -phenotypes: - -Text: -neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) -is caused by heterozygous mutation in the FRMD5 gene. -Neurodevelopmental disorder with eye movement abnormalities and ataxia (NEDEMA) -is characterized by global developmental delay apparent from infancy. -Affected individuals show delayed walking with an unsteady gait, variably impaired -intellectual development, learning disabilities, and speech difficulties. -Abnormal eye movements, which are often noted in early childhood, include opsoclonus, -nystagmus, and strabismus. Some patients have seizures, which may be refractor. -Lu et al. (2022) reported 8 unrelated patients, ranging in age from 3 to 27 years, -with a similar neurodevelopmental disorder and de novo heterozygous mutations in the FRMD5 gene. -The patients presented in infancy with global developmental delay and showed delayed walking, -variably impaired intellectual development, and poor or absent speech. -Those that achieved walking had an unsteady gait, and most had hypotonia and ataxia; -a few demonstrated spasticity. Some patients had dyslexia or learning disabilities. -Six patients had seizures or evidence of seizures, including 2 patients who were diagnosed -in infancy with refractory epilepsy and West syndrome. All patients had eye movement -abnormalities, ranging from strabismus and intermittent esotropia to opsoclonus and nystagmus. -Two were visually impaired and had myopia or hypermetropia. Brain imaging was -normal in most patients, but one had pachygyria and another had delayed myelination. -A few patients had additional features such as myoclonus, dystonia, dyskinesia, and -behavioral problems. -Inheritance: -### -""" - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.llm_client = OpenAIClient() - - def test_all_prompts(self): - """Test all prompts.""" - prompt_doc = yaml.safe_load(open(PROMPTS_FILE)) - default_engine = prompt_doc.get("default_engine", "gpt-3.5-turbo-instruct") - for prompt in prompt_doc["prompts"]: - prompt_text = prompt["prompt"] - if not isinstance(prompt_text, str): - prompt_text = yaml.dump(prompt_text) - engine = prompt.get("engine", default_engine) - client = OpenAIClient(model=engine) - pre_prompt = prompt.get("pre_prompt", "") - prompt_text = "".join([pre_prompt, prompt_text]) - print(f"## Testing prompt [{engine}: [{len(prompt_text)}] {prompt_text}") - ann = client.complete(prompt_text) - print(f"## Response: len={len(ann)}") - print(ann) - for expected in prompt.get("expected", []): - self.assertTrue(re.search(expected, ann, re.IGNORECASE)) - - def test_completion(self): - """Tests end to end knowledge extraction.""" - client = self.llm_client - ann = client.complete(PROMPT) - print(ann) - - def test_drug_mech_db(self): - """Test drug mechanism database.""" - client = self.llm_client - ann = client.complete( - """ - Explain the chain of events that relate a drug to a disease as a semi-colon separated list. - - Example: - - cortisone treats keratitis: - - cortisone increases glucocorticoid receptor; glucocorticoid receptor regulates COX; - COX regulates prostaglandin; prostaglandin regulates inflammation; - inflammation cause keratitis - - Text: - - imatinib treats chronic myeloid leukemia: - """ - ) - print(ann) - - def test_code_completion_generalization(self): - """Tests structured responses.""" - engine = "gpt-3.5-turbo" - client = OpenAIClient(model=engine) - print(len(CODE_PROMPT_GENERALIZATION)) - ann = client.complete(CODE_PROMPT_GENERALIZATION) - print(ann) - - def test_extract_via_code_completion(self): - """Tests structured responses.""" - engine = "gpt-3.5-turbo" - client = OpenAIClient(model=engine) - ann = client.complete(CODE_PROMPT_EXTRACT) - print(ann) - - @unittest.skip("Doesn't work well with current OpenAI API") - def test_fine_tuned(self): - engine = ( - "davinci:ft-lawrence-berkeley-national-laboratory:mendelian-disease-2022-12-22-00-53-36" - ) - client = OpenAIClient(model=engine) - ann = client.complete(TUNED_TEST_PROMPT) - print(ann) diff --git a/tests/integration/test_clients/test_pubmed_client.py b/tests/integration/test_clients/test_pubmed_client.py deleted file mode 100644 index 8104e12ed..000000000 --- a/tests/integration/test_clients/test_pubmed_client.py +++ /dev/null @@ -1,33 +0,0 @@ -"""PubMed client tests.""" -import unittest - -from talisman.clients import PubmedClient - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.client = PubmedClient() - - def test_lookup(self): - """Test PMID lookup.""" - text = self.client.text("PMID:28449677") - print(text) - - def test_multiple_lookup(self): - """Test lookup of multiple PMIDs.""" - text = self.client.text(["25662031", "28449677"]) - print(text) - - def test_malformed_lookup(self): - """Text lookup of invalid PMID.""" - text = self.client.text("jelly") - self.assertFalse(text) - - def test_search(self): - """Test PMID search.""" - print("Testing...") - results = list(self.client.search("Long covid", ["review", "treatment", "therapies"])) - print(results) diff --git a/tests/integration/test_evaluation/test_eval_ctd.py b/tests/integration/test_evaluation/test_eval_ctd.py deleted file mode 100644 index ba3a4887e..000000000 --- a/tests/integration/test_evaluation/test_eval_ctd.py +++ /dev/null @@ -1,89 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -from talisman.evaluation.ctd import eval_ctd -from talisman.evaluation.ctd.eval_ctd import EvalCTD -from talisman.io.yaml_wrapper import dump_minimal_yaml -from tests import OUTPUT_DIR - -EXTRACTIONS_OUT = OUTPUT_DIR / "eval-ctd-extractions.yaml" - -ALT_EXAMPLE = """Title: Cocaine induced myocardial ischemia. -Abstract: We report a case of myocardial ischemia induced by cocaine. -The ischemia probably induced by coronary artery spasm was reversed by -nitroglycerin and calcium blocking agents. -""" - -EXAMPLE = """Title: Downbeat nystagmus associated with intravenous patient-controlled -administration of morphine. -Abstract: IMPLICATIONS: This case documents a patient who developed dizziness with -downbeating nystagmus while receiving a relatively large dose of IV patient-controlled -analgesia morphine.Although there have been case reports of epidural morphine with these -symptoms and signs,this has not been previously documented with IV or patient-controlled -analgesia morphine. -""" - -logger = logging.getLogger(eval_ctd.__name__) -logger.setLevel(logging.INFO) - - -class TestCTD(unittest.TestCase): - """Test CTD evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalCTD() - - def test_load_test_sets(self): - docs = list(self.engine.load_test_cases()) - self.assertGreater(len(docs), 100) - for d in docs: - logger.debug(dump_minimal_yaml(d)) - - def test_eval(self): - evaluator = self.engine - evaluator.num_tests = 1 - eos = evaluator.eval() - with open(EXTRACTIONS_OUT, "w") as f: - f.write(dump_minimal_yaml(eos, minimize=False)) - # yaml.dump(eos.dict(), f) - - def test_individual_case(self): - evaluator = self.engine - ke = evaluator.extractor - r = ke.extract_from_text(EXAMPLE) - print(dump_minimal_yaml(r)) - - def test_is_valid_identifier(self): - evaluator = self.engine - ke = evaluator.extractor - chemical = ke.schemaview.get_class("Chemical") - disease = ke.schemaview.get_class("Disease") - cases = [ - ("MESH:C1", chemical, False, "too short"), - ("MESH:D009020", chemical, True, "valid chemical"), - ("MESH:D000071256", chemical, False, "too long"), - ("CHEBI:12345", chemical, False, "not an requested ID space"), - ("MESH:D054556", chemical, False, "disease"), - ("MESH:D054556", disease, True, "valid disease"), - ] - for case, cls, valid, reason in cases: - self.assertEqual(valid, ke.is_valid_identifier(case, cls), reason) - - def test_normalize_identifier(self): - evaluator = self.engine - ke = evaluator.extractor - chemical = ke.schemaview.get_class("Chemical") - disease = ke.schemaview.get_class("Disease") - cases = [ - ("CHEBI:17303", chemical, ["MESH:D009020"], "via node normalization"), - ("MESH:D009020", chemical, ["MESH:D009020"], "reflexive (chemical)"), - ("MESH:D054556", chemical, [], "disease"), - ("MESH:D054556", disease, ["MESH:D054556"], "reflexive (disease)"), - ("MESH:D009020", disease, [], "disease"), - ] - for case, cls, expected, reason in cases: - normalized = list(ke.normalize_identifier(case, cls)) - print(normalized) - self.assertCountEqual(expected, normalized, reason) diff --git a/tests/integration/test_evaluation/test_eval_drugmechdb.py b/tests/integration/test_evaluation/test_eval_drugmechdb.py deleted file mode 100644 index 301203dd7..000000000 --- a/tests/integration/test_evaluation/test_eval_drugmechdb.py +++ /dev/null @@ -1,178 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml - -from talisman.engines.spires_engine import SPIRESEngine -from talisman.evaluation.drugmechdb.datamodel.drugmechdb import Graph, Mechanism -from talisman.evaluation.drugmechdb.eval_drugmechdb import EvalDrugMechDB, _fix_source_mechanism -from tests import OUTPUT_DIR - -NORMALIZED_OUT = OUTPUT_DIR / "drugmechdb-normalized.yaml" -PREDICTIONS_OUT = OUTPUT_DIR / "eval-drugmechdb-predictions.yaml" -EXTRACTION_OUT = OUTPUT_DIR / "eval-drugmechdb-extraction.yaml" -TRAINING_OUT = OUTPUT_DIR / "training-drugmechdb.yaml" - -EXAMPLE_SOURCE = """ -- directed: true - graph: - _id: DB00316_MESH_D018771_1 - disease: Arthralgia - disease_mesh: MESH:D018771 - drug: Acetaminophen - drug_mesh: MESH:D000082 - drugbank: DB:DB00316 - links: - - key: decreases activity of - source: MESH:D000082 - target: UniProt:P23219 - - key: decreases activity of - source: MESH:D000082 - target: UniProt:P35354 - - key: decreases activity of - source: MESH:D000082 - target: UniProt:Q15185 - - key: positively regulates - source: UniProt:P23219 - target: GO:0001516 - - key: positively regulates - source: UniProt:P35354 - target: GO:0001516 - - key: positively regulates - source: UniProt:Q15185 - target: GO:0001516 - - key: increases abundance of - source: GO:0001516 - target: MESH:D011453 - - key: positively correlated with - source: MESH:D011453 - target: MESH:D018771 - multigraph: true - nodes: - - id: MESH:D000082 - label: Drug - name: Acetaminophen - - id: UniProt:P23219 - label: Protein - name: Prostaglandin G/H synthase 1 - - id: UniProt:P35354 - label: Protein - name: Prostaglandin G/H synthase 2 - - id: UniProt:Q15185 - label: Protein - name: Prostaglandin E synthase 3 - - id: GO:0001516 - label: BiologicalProcess - name: prostaglandin biosynthetic process - - id: MESH:D011453 - label: ChemicalSubstance - name: Prostaglandins - - id: MESH:D018771 - label: Disease - name: Arthralgia - reference: - - https://go.drugbank.com/drugs/DB00316#mechanism-of-action - - https://www.uniprot.org/uniprot/P23219#function - - https://www.uniprot.org/uniprot/P35354#function - - https://www.uniprot.org/uniprot/Q15185#function - - https://en.wikipedia.org/wiki/Arthralgia -""" - - -class TestDrugMechDB(unittest.TestCase): - """Test GO evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalDrugMechDB() - - def test_data_model(self): - g = Graph(id="x") - m = Mechanism( - directed=True, - graph={ - "id": "DB11888_MESH_D007251_1", - }, - ) - - def test_load_exemplars(self): - mechanisms = self.engine.load_exemplars() - objs = [m.dict() for m in mechanisms] - print(yaml.dump(objs[0:5])) - self.assertGreater(len(mechanisms), 0) - - def test_transform(self): - objs = yaml.safe_load(EXAMPLE_SOURCE) - obj = _fix_source_mechanism(objs[0]) - src_mechanism = Mechanism(**obj) - r = self.engine.transform_mechanism(src_mechanism) - print(yaml.dump(r.dict())) - - def test_load_and_transform_source_database(self): - """ - Tests the ability to translate the source DrugMechDB yaml into Llama model. - - This is currently slow: this test may be skipped. - - If the source YAML changes, then re-run this and copy the file from - the output directory (drugmechdb-normalized.yaml) to - - :return: - """ - mechanisms = self.engine.load_and_transform_source_database() - print(f"Loaded {len(mechanisms)} mechanisms") - objs = [m.dict() for m in mechanisms] - with open(NORMALIZED_OUT, "w") as f: - yaml.dump(objs, f) - print(yaml.dump(objs[0:5])) - self.assertGreater(len(mechanisms), 0) - - def test_load_target_database(self): - mechanisms = self.engine.load_target_database() - print(f"Loaded {len(mechanisms)} mechanisms") - objs = [m.dict() for m in mechanisms[0:5]] - print(yaml.dump(objs)) - self.assertGreater(len(mechanisms), 0) - - def test_drug_to_mechanism_text(self): - self.assertTrue( - self.engine.drug_to_mechanism_text["drugbank:DB00005"].startswith( - "There are two distinct receptors" - ) - ) - - def test_training_set(self): - evaluator = self.engine - ke = evaluator.extractor - training_set = list(evaluator.create_training_set(100)) - t = dict(base_model="gpt-3.5-turbo-instruct", template=ke.template, examples=training_set) - with open(TRAINING_OUT, "w") as f: - yaml.dump(t, f) - # print(yaml.dump(training_set)) - - def test_eval_extraction(self): - evaluator = self.engine - evaluator.num_tests = 100 - eos = evaluator.eval() - with open(EXTRACTION_OUT, "w") as f: - yaml.dump(eos.dict(), f) - - @unittest.skip("Skip this test because it takes a long time and is more expensive") - def test_eval_fine_tuned_extraction(self): - evaluator = EvalDrugMechDB() - ft = "davinci:ft-lawrence-berkeley-national-laboratory:drugmechdb-001-2022-12-22-02-25-40" - evaluator.extractor = SPIRESEngine("drug.DrugMechanism", engine=ft) - evaluator.num_tests = 40 - eos = evaluator.eval() - with open(EXTRACTION_OUT, "w") as f: - yaml.dump(eos.dict(), f) - - def test_eval_generalize(self): - evaluator = self.engine - evaluator.num_tests = 3 - evaluator.num_training = 3 - mechanisms = self.engine.load_exemplars() - evaluator.data = mechanisms - eos = evaluator.eval_path_prediction() - with open(PREDICTIONS_OUT, "w") as f: - yaml.dump(eos.dict(), f) diff --git a/tests/integration/test_evaluation/test_eval_go.py b/tests/integration/test_evaluation/test_eval_go.py deleted file mode 100644 index 7014448a5..000000000 --- a/tests/integration/test_evaluation/test_eval_go.py +++ /dev/null @@ -1,43 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml - -from talisman.evaluation.go.eval_go import EvalGO, EvaluationObjectSetGO -from talisman.templates.metabolic_process import MetabolicProcess -from tests import OUTPUT_DIR - -EXAMPLES_OUT = OUTPUT_DIR / "eval-go-examples.yaml" -PREDICTIONS_OUT = OUTPUT_DIR / "eval-go-predictions.yaml" - - -class TestEvalGO(unittest.TestCase): - """Test GO evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalGO() - - def test_dm(self): - mp = MetabolicProcess( - id="GO:0008152", - ) - eos = EvaluationObjectSetGO(test=[mp], training=[]) - print(yaml.dump(eos.dict())) - - def test_create_test_and_training(self): - engine = self.engine - ke = engine.extractor - eos = engine.create_test_and_training() - with open(EXAMPLES_OUT, "w") as f: - yaml.dump(eos.dict(), f) - for t in eos.test: - print(yaml.dump(t.dict())) - ser = ke.serialize_object(t) - print(f"Serialized: {ser}") - - def test_eval_predictions(self): - engine = self.engine - eos = engine.eval() - with open(PREDICTIONS_OUT, "w") as f: - yaml.dump(eos.dict(), f) diff --git a/tests/integration/test_evaluation/test_eval_hpoa.py b/tests/integration/test_evaluation/test_eval_hpoa.py deleted file mode 100644 index e4dc88193..000000000 --- a/tests/integration/test_evaluation/test_eval_hpoa.py +++ /dev/null @@ -1,67 +0,0 @@ -"""Core tests for Human Phenotype Ontology Annotations (HPOA) evaluation.""" -import unittest - -import yaml - -from talisman.evaluation.hpoa.eval_hpoa import EvalHPOA -from tests import OUTPUT_DIR - -NORMALIZED_OUT = OUTPUT_DIR / "hpoa-normalized.yaml" -PREDICTIONS_OMIM_OUT = OUTPUT_DIR / "eval-hpoa-predictions-omim.yaml" -PREDICTIONS_PUBS_OUT = OUTPUT_DIR / "eval-hpoa-predictions-pubs.yaml" -PREDICTIONS_ALL_OUT = OUTPUT_DIR / "eval-hpoa-predictions-all.yaml" - - -class Testhpoa(unittest.TestCase): - """Test HPOA evaluation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - self.engine = EvalHPOA() - - def test_load_hpoa(self): - diseases = self.engine.annotations_to_diseases() - objs = [m.model_dump() for m in diseases] - print(yaml.dump(objs[0:3])) - self.assertGreater(len(diseases), 0) - - def test_diseases(self): - diseases = self.engine.diseases() - for test_case in diseases[0:2]: - text = self.engine.disease_text(test_case.id) - self.assertIsNotNone(text) - self.assertGreater(len(text), 100) - objs = [m.model_dump() for m in diseases] - print(yaml.dump(objs[0:3])) - self.assertGreater(len(diseases), 0) - - def test_diseases_by_publication(self): - t2d = self.engine.diseases_by_publication() - t2d_sample = {k: t2d[k] for k in list(t2d)[0:2]} - for k, disease in t2d_sample.items(): - text = self.engine.disease_text(disease.id) - self.assertIsNotNone(text) - self.assertGreater(len(text), 100) - print(f"## {k}: {disease.id} ") - print(yaml.dump(disease.model_dump())) - - def test_eval_pubs(self): - evaluator = self.engine - eos = evaluator.eval("pubs") - with open(PREDICTIONS_PUBS_OUT, "w") as f: - yaml.dump(eos.model_dump(), f) - - @unittest.skip("Need to retrieve more OMIM texts - stochastic") - def test_eval_all(self): - evaluator = self.engine - eos = evaluator.eval("all") - with open(PREDICTIONS_ALL_OUT, "w") as f: - yaml.dump(eos.model_dump(), f) - - @unittest.skip("Need to retrieve more OMIM texts - stochastic") - def test_eval_omim(self): - """Evaluates extraction purely from OMIM texts.""" - evaluator = self.engine - eos = evaluator.eval("omim") - with open(PREDICTIONS_OMIM_OUT, "w") as f: - yaml.dump(eos.model_dump(), f) diff --git a/tests/integration/test_knowledge_engines/test_cases.py b/tests/integration/test_knowledge_engines/test_cases.py deleted file mode 100644 index 17bdff6da..000000000 --- a/tests/integration/test_knowledge_engines/test_cases.py +++ /dev/null @@ -1,69 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from talisman.engines.spires_engine import SPIRESEngine -from talisman.io.yaml_wrapper import dump_minimal_yaml -from tests import CASES_DIR, OUTPUT_DIR - -CASES = [ - ("recipe", "recipe-palak-paneer"), - ("treatment", "treatment-schiz"), - ("recipe.Recipe", "recipe-spaghetti"), - ("recipe.Recipe", "recipe-tortilla-soup"), - ("recipe.Recipe", "recipe-egg-noodles"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-cmt2e-summary"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-cmt2e"), - ("drug.DrugMechanism", "drug-DB00316-moa"), - ("metagenome_study.Study", "environment-jgi2"), - ("environmental_sample.Study", "environment-jgi1"), - ("reaction.ReactionDocument", "reaction-20657015"), - ("reaction.GeneToReaction", "reaction-21290071"), - ("gocam.GoCamAnnotations", "gocam-27929086"), - ("gocam.GoCamAnnotations", "gocam-33246504"), - ("gocam.GoCamAnnotations", "gocam-betacat"), - ("environmental_sample.Study", "environmental-sample-hyporheic"), - ("treatment.DiseaseTreatmentSummary", "treatment-marfan"), - ("treatment.DiseaseTreatmentSummary", "treatment-eds"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-sly"), - ("mendelian_disease.MendelianDisease", "mendelian-disease-marfan"), - ("environmental_sample.Study", "amphibian_skin"), - ("environmental_sample.Study", "human_urban_green_space"), - ("environmental_sample.Study", "human_smoking_China"), -] - - -class TestCases(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - ke_map = {} - for template, _ in CASES: - ke_map[template] = SPIRESEngine(template, recurse=True, auto_prefix="AUTO") - self.ke_map = ke_map - - def test_cases(self): - """Tests end to end knowledge extraction.""" - for template, input_name in CASES: - ke = self.ke_map[template] - input_file = CASES_DIR / f"{input_name}.txt" - ann = ke.extract_from_file(input_file) - # print(yaml.dump(ann.dict())) - # for ne in ke.named_entities: - # print(yaml.dump(ne.dict())) - # result_dict = { - # "input_file": str(input_file), - # "text": ke.last_text, - # "results": ann.dict(), - # "named_entities": [ne.dict() for ne in ke.named_entities], - # } - # print(yaml.dump(result_dict)) - output_file = str(OUTPUT_DIR / f"{input_name}.yaml") - print(f"Writing {output_file}") - with open(output_file, "w", encoding="utf-8") as f: - f.write(dump_minimal_yaml(ann)) - pkl_output_file = str(OUTPUT_DIR / f"{input_name}.pickle") - print(f"Writing {pkl_output_file}") - with open(pkl_output_file, "wb") as f: - f.write(pickle.dumps(ann)) diff --git a/tests/integration/test_knowledge_engines/test_generalizations.py b/tests/integration/test_knowledge_engines/test_generalizations.py deleted file mode 100644 index 905735386..000000000 --- a/tests/integration/test_knowledge_engines/test_generalizations.py +++ /dev/null @@ -1,89 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml -from oaklib import get_implementation_from_shorthand - -from talisman.engines.spires_engine import SPIRESEngine -from tests import INSTANCES_DIR, OUTPUT_DIR - -CASES = [ - ( - "drug.DrugMechanism", - [{"disease": "MESH:D014552", "drug": "drugbank:DB00438"}], - [ - ["disease", "drug"], - ], - [ - "sqlite:obo:mesh", - "sqlite:obo:drugbank", - "sqlite:obo:go", - "sqlite:obo:uberon", - "sqlite:obo:pr", - ], - "drug-mechanisms-001", - ), - ( - "reaction.Reaction", - [ - { - "label": "pseudouridine 5'-phosphatase activity", - "description": "Catalysis of the reaction:\ - pseudouridine 5'-phosphate + H2O = pseudouridine + phosphate.", - }, - { - "label": "L-altrarate dehydratase activity", - "description": "Catalysis of the reaction:\ - L-altrarate = 5-dehydro-4-deoxy-D-glucarate + H2O.", - }, - # rhea:40031 - {"description": "ent-copalyl diphosphate + H2O = diphosphate + ent-manool"}, - ], - [ - ["label"], - ["description"], - ["label", "description"], - ], - [], - "reactions-001", - ), -] - - -class TestGeneralize(unittest.TestCase): - """Test generalization.""" - - def setUp(self) -> None: - """Set up all engines in advance.""" - ke_map = {} - for c in CASES: - template = c[0] - ke_map[template] = SPIRESEngine(template) - self.ke_map = ke_map - - def test_cases(self): - """Tests generalization over all cases.""" - for template, objs, combos, labelers, input_file in CASES: - ke = self.ke_map[template] - ke.labelers = [get_implementation_from_shorthand(labeler) for labeler in labelers] - print(f"Loading {input_file}") - with open(INSTANCES_DIR / f"{input_file}.yaml") as f: - examples = yaml.safe_load(f) - print(examples) - nu_objs = [] - for obj in objs: - for combo in combos: - if any(c not in obj for c in combo): - continue - print(f"Testing {combo}") - test_obj = {k: obj[k] for k in combo} - nu_obj = ke.generalize(test_obj, examples) - print(nu_obj) - nu_obj = nu_obj.dict() - nu_obj["_combo"] = list(combo) - nu_obj["_input"] = test_obj - nu_objs.append(nu_obj) - with open( - str(OUTPUT_DIR / f"generalized-{input_file}.yaml"), "w", encoding="utf-8" - ) as f: - yaml.dump(nu_objs, f) diff --git a/tests/integration/test_knowledge_engines/test_gpt4all_engine.py b/tests/integration/test_knowledge_engines/test_gpt4all_engine.py deleted file mode 100644 index 937c809a2..000000000 --- a/tests/integration/test_knowledge_engines/test_gpt4all_engine.py +++ /dev/null @@ -1,33 +0,0 @@ -"""Tests for using local GGML models.""" -import unittest - -import yaml - -from talisman.engines.gpt4all_engine import GPT4AllEngine - -TEMPLATE = "mendelian_disease.MendelianDisease" - -# This is a small test model. It doesn't really -# do extraction - it's a BERT model for sentence -# embeddings - but it tests functionality. -TEST_MODEL = "ggml-all-MiniLM-L6-v2-f16" - -TEXT_INPUT = "Peanut butter and cheese" - - -class TestCore(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.ke = GPT4AllEngine(template=TEMPLATE, model=TEST_MODEL) - - def test_extract(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - ann = ke.extract_from_text(TEXT_INPUT) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - results = ann.extracted_object - if results is not None: - raise ValueError(f"Unexpected output type, got {type(results)}") diff --git a/tests/integration/test_knowledge_engines/test_halo_engine.py b/tests/integration/test_knowledge_engines/test_halo_engine.py deleted file mode 100644 index 8bbe5c72e..000000000 --- a/tests/integration/test_knowledge_engines/test_halo_engine.py +++ /dev/null @@ -1,88 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -import yaml -from oaklib import get_implementation_from_shorthand -from oaklib.datamodels.vocabulary import IS_A, PART_OF - -from talisman.converters.ontology_converter import OntologyConverter -from talisman.engines import halo_engine -from talisman.engines.halo_engine import HALOEngine -from talisman.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR, OUTPUT_DIR - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" -TEST_ONTOLOGY_HALO = INPUT_DIR / "go-nucleus.halo.yaml" -TEST_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.halo.yaml" -HALLUCINATED_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.hallucinated.halo.yaml" - -logger = logging.getLogger(halo_engine.__name__) -logger.setLevel(level=logging.INFO) - - -class TestHALO(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.ke = HALOEngine( - expand_horizon=False, - fixed_slot_values={"context": "subcellular"}, - ) - self.ke.seed_from_file(TEST_ONTOLOGY_HALO) - adapter = get_implementation_from_shorthand(str(TEST_ONTOLOGY_OAK)) - self.converter = OntologyConverter(adapter) - - @unittest.skip("Algorithm changed") - def test_get_candidate_elements(self): - ke = self.ke - elts = ke.get_candidate_elements() - print(len(elts)) - self.assertGreater(len(elts), 10) - print(elts[0:5]) - - def test_hallucinate_element(self): - ke = self.ke - candidates = set(ke.get_candidate_elements()) - name = "Axon" - elt = ke.hallucinate_element(name) - print("## ELEMENT:") - print(yaml.dump(elt.dict())) - [elt2] = [elt for elt in ke.ontology.elements if elt.name == name] - self.assertEqual(elt, elt2) - self.assertIn(name, ke.visited) - next_candidates = set(ke.get_candidate_elements()) - new_candidates = next_candidates.difference(candidates) - print(f"New candidates={new_candidates}") - self.assertGreater(len(new_candidates), 0) - # ensure that new ones are added to the end - self.assertIn(ke.get_candidate_elements()[-1], new_candidates) - - def test_hallucinate(self): - ke = self.ke - elts = ke.hallucinate(["Axon", "Dendrite"], num_iterations=4) - for e in elts: - print(f"{e.name} {e.description}") - print(f"ELTS: {len(elts)}") - with open(HALLUCINATED_ONTOLOGY_OUTPUT, "w") as f: - f.write(dump_minimal_yaml(ke.ontology)) - - def test_hallucinate_metabolism(self): - ke = HALOEngine( - expand_horizon=False, - fixed_slot_values={"context": "metabolism"}, - ) - preds = [IS_A, PART_OF] - adapter = get_implementation_from_shorthand("sqlite:obo:go") - converter = OntologyConverter(adapter) - ke.ontology = converter.extract_seed_ontology(["GO:0034651", "GO:0034653"], preds) - elts = ke.hallucinate( - ["KetoaldopentoseBiosyntheticProcess", "IsomaltotrioseMetabolicProcess"], - num_iterations=3, - ) - for e in elts: - print(f"{e.name} {e.description}") - print(f"ELTS: {len(elts)}") - with open(str(OUTPUT_DIR / "carbohydrate-metabolism.hallucinated.halo.yaml"), "w") as f: - f.write(dump_minimal_yaml(ke.ontology)) diff --git a/tests/integration/test_knowledge_engines/test_mapping.py b/tests/integration/test_knowledge_engines/test_mapping.py deleted file mode 100644 index ae0c9c21c..000000000 --- a/tests/integration/test_knowledge_engines/test_mapping.py +++ /dev/null @@ -1,157 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -from oaklib import get_adapter -from sssom.parsers import parse_sssom_table, to_mapping_set_document -from sssom_schema import Mapping - -from talisman.clients import openai_client -from talisman.engines import mapping_engine -from talisman.engines.mapping_engine import CategorizedMapping, MappingEngine, MappingTaskCollection -from talisman.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" - -HEART = "UBERON:0000948" -NECK_OF_ORGAN = "UBERON:0001560" -MA_NECK_ORGAN = "MA:0000589" -MA_HEART = "MA:0000072" - -ENVO_MOUTH = "ENVO:00000479" # river mouth -WIKIDATA_MOUTH = "wikidata:Q9635" # anatomical mouth -UBERON_MOUTH = "UBERON:0000165" # anatomical mouth -UBERON_ORAL_OPENING = "UBERON:0000166" - -logger = logging.getLogger(mapping_engine.__name__) -client_logger = logging.getLogger(openai_client.__name__) - -client_logger.setLevel(logging.DEBUG) - - -def _show(mapping_eval: CategorizedMapping): - print(f"{mapping_eval.subject} -> {mapping_eval.object}") - print(mapping_eval.completion) - print(dump_minimal_yaml(mapping_eval.dict())) - - -class TestMapping(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up OAK adapter, extractor, and reasoner.""" - subject_adapter = get_adapter("sqlite:obo:uberon") - object_adapter = get_adapter("sqlite:obo:zfa") - self.mapper = MappingEngine(subject_adapter=subject_adapter, object_adapter=object_adapter) - - def test_generate(self): - mapper = self.mapper - subjects = [HEART] - tc = MappingTaskCollection(name="test", subjects=subjects, object_sources=["ZFA"]) - tasks = list(mapper.generate_tasks(tc)) - for task in tasks: - print(dump_minimal_yaml(task.dict())) - tc.tasks = tasks - results = list(mapper.run_tasks(tc)) - for result in results: - print(dump_minimal_yaml(result.dict())) - - def test_from_sssom(self): - mapper = self.mapper - - def _exclude_trivial(m: Mapping) -> bool: - return m.subject_label.lower() == m.object_label.lower() - - tc = mapper.from_sssom( - INPUT_DIR / "mondo-exact-ncit.sssom.tsv", exclude_functions=[_exclude_trivial] - ) - # print(dump_minimal_yaml(tc.dict())) - results = list(mapper.run_tasks(tc)) - for result in results: - print(dump_minimal_yaml(result.dict())) - - def test_from_sssom2(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:mondo"), - object_adapter=get_adapter("sqlite:obo:ncit"), - ) - - msdf = parse_sssom_table(INPUT_DIR / "mondo-exact-ncit.sssom.tsv") - msd = to_mapping_set_document(msdf) - - def _exclude_trivial(m: Mapping) -> bool: - return m.subject_label.lower() == m.object_label.lower() - - for m in msd.mapping_set.mappings: - if _exclude_trivial(m): - continue - m2 = mapper.categorize_sssom_mapping(m) - print(m2) - - def test_mapping_eval(self): - """Test evaluation of mapping on uberon.""" - mapper = self.mapper - subjects = [HEART] - for meval in mapper.categorize_mappings(subjects, object_sources=["ZFA"]): - _show(meval) - - def test_different_from(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:ma"), - ) - subjects = [NECK_OF_ORGAN] - objects = [MA_NECK_ORGAN] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - def test_very_different_from(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:ma"), - ) - subjects = [HEART] - objects = [MA_NECK_ORGAN] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - def test_very_different_from2(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:envo"), - ) - subjects = [UBERON_MOUTH, UBERON_ORAL_OPENING] - objects = [ENVO_MOUTH] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - def test_species_identical(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:uberon"), - object_adapter=get_adapter("sqlite:obo:ma"), - ) - subjects = [HEART] - objects = [MA_HEART] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) - - @unittest.skip("Requires new OAK release") - def test_wikidata(self): - mapper = MappingEngine( - subject_adapter=get_adapter("sqlite:obo:envo"), object_adapter=get_adapter("wikidata:") - ) - subjects = [ENVO_MOUTH] - objects = [WIKIDATA_MOUTH] - for subject in subjects: - for object in objects: - meval = mapper.categorize_mapping(subject, object) - _show(meval) diff --git a/tests/integration/test_knowledge_engines/test_pheno.py b/tests/integration/test_knowledge_engines/test_pheno.py deleted file mode 100644 index a18d2b74d..000000000 --- a/tests/integration/test_knowledge_engines/test_pheno.py +++ /dev/null @@ -1,37 +0,0 @@ -"""Core tests.""" -import json -import logging -import unittest - -from oaklib import get_adapter - -from talisman.clients import openai_client -from talisman.engines import mapping_engine -from talisman.engines.pheno_engine import PhenoEngine -from talisman.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR - -PHENOPACKET_FILE = INPUT_DIR / "Guo-2017-EXTL3-Patient_1.json" - -logger = logging.getLogger(mapping_engine.__name__) -client_logger = logging.getLogger(openai_client.__name__) - -# client_logger.setLevel(logging.DEBUG) - - -class TestPhenopackets(unittest.TestCase): - def setUp(self) -> None: - """Set up OAK adapter, extractor, and reasoner.""" - self.adapter = get_adapter("sqlite:obo:hp") - - def test_diagnose(self): - phenopacket = json.load(open(PHENOPACKET_FILE)) - engine = PhenoEngine() - result = engine.predict_disease(phenopacket) - print(result) - - def test_eval(self): - phenopacket = json.load(open(PHENOPACKET_FILE)) - engine = PhenoEngine() - results = engine.evaluate([phenopacket]) - print(dump_minimal_yaml(results)) diff --git a/tests/integration/test_knowledge_engines/test_reasoning.py b/tests/integration/test_knowledge_engines/test_reasoning.py deleted file mode 100644 index 8480f82c0..000000000 --- a/tests/integration/test_knowledge_engines/test_reasoning.py +++ /dev/null @@ -1,188 +0,0 @@ -"""Core tests.""" -import logging -import unittest -from typing import Iterator, List - -import yaml -from oaklib import get_adapter -from oaklib.datamodels.vocabulary import IS_A, PART_OF -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from talisman.engines.reasoner_engine import ReasonerEngine, ReasonerResult, ReasonerResultSet -from talisman.io.csv_wrapper import write_obj_as_csv -from talisman.io.yaml_wrapper import dump_minimal_yaml -from talisman.ontex import extractor -from talisman.ontex.extractor import OntologyExtractor, Task -from tests import ( - BIOLOGICAL_PROCESS, - CELLULAR_ANATOMICAL_ENTITY, - CELLULAR_ORGANISMS, - ENVELOPE, - FUNGI, - IMBO, - INPUT_DIR, - MAMMALIA, - MEMBRANE, - NUCLEAR_ENVELOPE, - NUCLEAR_MEMBRANE, - NUCLEUS, - ORGANELLE, - OUTPUT_DIR, - PLASMA_MEMBRANE, - VACUOLE, -) - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" - - -logger = logging.getLogger(extractor.__name__) -logger.setLevel(level=logging.INFO) - - -class TestReasoning(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up OAK adapter, extractor, and reasoner.""" - self.adapter = get_adapter(str(TEST_ONTOLOGY_OAK)) - if not isinstance(self.adapter, OboGraphInterface): - raise ValueError("Not an OboGraphInterface") - self.extractor = OntologyExtractor(adapter=self.adapter) - self.reasoner = ReasonerEngine() - # self.reasoner.client.model = "gpt-4" - - def save(self, results: List[ReasonerResult], name: str): - rset = ReasonerResultSet(name=name, results=results) - model = self.reasoner.client.model - with open(OUTPUT_DIR / f"reasoner-{name}-{model}.yaml", "w") as f: - f.write(dump_minimal_yaml(rset)) - path = str(OUTPUT_DIR / f"reasoner-{name}-{model}.tsv") - write_obj_as_csv(results, path) - - def tasks(self) -> Iterator[Task]: - extractor = self.extractor - # yield extractor.extract_indirect_superclasses_task( - # name="random", - # select_random=True, - # ) - yield extractor.extract_transitive_superclasses_task( - name="transitive-ancestor-nucleus", - subclass=NUCLEUS, - siblings=[VACUOLE], - roots=[ORGANELLE], - ) - yield extractor.extract_indirect_superclasses_task( - name="indirect-ancestor-nucleus", - subclass=NUCLEUS, - siblings=[VACUOLE], - roots=[ORGANELLE], - ) - yield extractor.extract_transitive_superclasses_task( - name="transitive-ancestor-nuclear-membrane", - subclass=IMBO, - siblings=[NUCLEUS], - roots=[ORGANELLE, BIOLOGICAL_PROCESS], - ) - yield extractor.extract_indirect_superclasses_task( - name="indirect-ancestor-nuclear-membrane", - subclass=IMBO, - siblings=[NUCLEUS], - roots=[ORGANELLE, BIOLOGICAL_PROCESS], - ) - yield extractor.extract_indirect_superclasses_task( - name="ancestor-nuclear-envelope", - subclass=NUCLEAR_MEMBRANE, - siblings=[NUCLEAR_ENVELOPE], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ) - yield extractor.extract_indirect_superclasses_task( - name="ancestor-human", - subclass=IMBO, - siblings=[NUCLEUS], - roots=[ORGANELLE, BIOLOGICAL_PROCESS], - ) - yield extractor.extract_most_recent_common_subsumers_task( - name="mrca-nucleus-vacuole", - subclass1=NUCLEUS, - subclass2=VACUOLE, - siblings=[NUCLEAR_MEMBRANE], - roots=[], - ) - yield extractor.extract_subclass_of_expression_task( - name="subclass-of-part-of-nuclear-envelope", - superclass=NUCLEUS, - predicate=PART_OF, - siblings=[VACUOLE], - ) - yield extractor.extract_incoherent_ontology_task( - name="incoherent-nucleus", - incoherents=[NUCLEUS], - siblings=[VACUOLE], - disjoints=[(ORGANELLE, ENVELOPE)], - spiked_relationships=[(NUCLEUS, IS_A, NUCLEAR_MEMBRANE)], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ) - yield extractor.extract_incoherent_ontology_task( - name="incoherent-plasma-membrane", - incoherents=[PLASMA_MEMBRANE], - siblings=[NUCLEUS], - disjoints=[(ORGANELLE, MEMBRANE)], - spiked_relationships=[(PLASMA_MEMBRANE, IS_A, ORGANELLE)], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ) - yield extractor.extract_incoherent_ontology_task( - name="incoherent-ok-organism", - incoherents=[], - siblings=[], - disjoints=[(MAMMALIA, FUNGI)], - spiked_relationships=[], - roots=[CELLULAR_ORGANISMS], - ) - - def test_reason(self): - """Test basic reasoning, no explanations.""" - reasoner = self.reasoner - results = [] - for task in self.tasks(): - result = reasoner.reason(task) - print(yaml.dump(result.dict(), sort_keys=False)) - print(result.prompt) - results.append(result) - ReasonerResultSet(results=[result]) - for result in results: - print( - f"Result: {result.jaccard_score} {result.false_positives} {result.false_negatives}" - ) - self.save(results, "basic") - - def test_reason_with_explanations(self): - """Test reasoning with explanations included.""" - reasoner = self.reasoner - results = [] - for task in self.tasks(): - task.include_explanations = True - result = reasoner.reason(task) - print(result.prompt) - print(yaml.dump(result.dict(), sort_keys=False)) - results.append(result) - for result in results: - print( - f"Result: {result.jaccard_score} {result.false_positives} {result.false_negatives}" - ) - self.save(results, "explanation") - - def test_reason_with_chain_of_thought(self): - """Test reasoning with explicit chain-of-thought trigger.""" - reasoner = self.reasoner - results = [] - for task in self.tasks(): - task.chain_of_thought = True - result = reasoner.reason(task) - print(result.prompt) - print(yaml.dump(result.dict(), sort_keys=False)) - results.append(result) - for result in results: - print( - f"Result: {result.jaccard_score} {result.false_positives} {result.false_negatives}" - ) - self.save(results, "chain-of-thought") diff --git a/tests/integration/test_knowledge_engines/test_spires_engine.py b/tests/integration/test_knowledge_engines/test_spires_engine.py deleted file mode 100644 index 4df876da9..000000000 --- a/tests/integration/test_knowledge_engines/test_spires_engine.py +++ /dev/null @@ -1,448 +0,0 @@ -"""Core tests.""" -import unittest - -import yaml -from linkml_runtime.linkml_model import ClassDefinitionName -from oaklib import get_implementation_from_shorthand - -from talisman.clients.pubmed_client import PubmedClient -from talisman.engines import create_engine -from talisman.engines.knowledge_engine import chunk_text -from talisman.engines.spires_engine import SPIRESEngine -from talisman.io.yaml_wrapper import dump_minimal_yaml -from talisman.templates.biological_process import BiologicalProcess -from talisman.templates.gocam import ( - ExtractionResult, - Gene, - GeneLocation, - GeneOrganismRelationship, - GoCamAnnotations, -) - -TEMPLATE = "gocam.GoCamAnnotations" - -PAPER = """ -Title: β-Catenin Is Required for the cGAS/STING Signaling Pathway but - Antagonized by the Herpes Simplex Virus 1 US3 Protein. -Text: -The cGAS/STING-mediated DNA-sensing signaling pathway is crucial -for interferon (IFN) production and host antiviral -responses. Herpes simplex virus I (HSV-1) is a DNA virus that has -evolved multiple strategies to evade host immune responses. Here, -we demonstrate that the highly conserved β-catenin protein in the -Wnt signaling pathway is an important factor to enhance the -transcription of type I interferon (IFN-I) in the cGAS/STING -signaling pathway, and the production of IFN-I mediated by -β-catenin was antagonized by HSV-1 US3 protein via its kinase -activity. Infection by US3-deficienct HSV-1 and its kinase-dead -variants failed to downregulate IFN-I and IFN-stimulated -gene (ISG) production induced by β-catenin. Consistent with this, -absence of β-catenin enhanced the replication of US3-deficienct -HSV-1, but not wild-type HSV-1. The underlying mechanism was the -interaction of US3 with β-catenin and its hyperphosphorylation of -β-catenin at Thr556 to block its nuclear translocation. For the -first time, HSV-1 US3 has been shown to inhibit IFN-I production -through hyperphosphorylation of β-catenin and to subvert host -antiviral innate immunity.IMPORTANCE Although increasing evidence -has demonstrated that HSV-1 subverts host immune responses and -establishes lifelong latent infection, the molecular mechanisms -by which HSV-1 interrupts antiviral innate immunity, especially -the cGAS/STING-mediated cellular DNA-sensing signaling pathway, -have not been fully explored. Here, we show that β-catenin -promotes cGAS/STING-mediated activation of the IFN pathway, which -is important for cellular innate immune responses and intrinsic -resistance to DNA virus infection. The protein kinase US3 -antagonizes the production of IFN by targeting β-catenin via its -kinase activity. The findings in this study reveal a novel -mechanism for HSV-1 to evade host antiviral immunity and add new -knowledge to help in understanding the interaction between the -host and HSV-1 infection. - -Keywords: HSV-1; US3; type I IFN; β-catenin. -""" - -EXAMPLE_RESULTS = """ -genes: β-Catenin; cGAS; STING; US3; IFN; ISG -organisms: Herpes Simplex Virus I (HSV-1); -gene_organisms: β-Catenin:host; cGAS:host; STING:host; US3:HSV-1; IFN:host; ISG:host -activities: production of type I IFN; transcription of type I IFN; replication of HSV-1; -nuclear translocation of β-catenin. -gene_functions: β-catenin:enhance the transcription of type I IFN; US3:antagonize -the production of IFN; β-catenin:block nuclear translocation. -cellular_processes: cGAS/STING-mediated DNA-sensing signaling; activation of IFN pathway -pathways: IFN pathway; Wnt signalling pathway -gene_gene_interactions: US3:β-catenin -gene_localizations: US3:host; β-catenin:host -""" - -EXAMPLE_RESULTS_ALT = """ -genes: β-Catenin; cGAS; STING; US3; IFN; ISG -organisms: Herpes Simplex Virus I (HSV-1); -gene_organisms: β-Catenin - Human; cGAS - Human; STING - Human; -US3 - Human; IFN - Human; ISG - Human. -activities: Transcription; Production; Downregulation; Replication; Nuclear Translocation -gene_functions: β-Catenin - Enhances Transcription; US3 - Antagonizes Production; -US3 - Downregulates IFN-I; US3 - Blocks Nuclear Translocation; β-Catenin - Enhances Production -cellular_processes: DNA-sensing; Interferon Production; Antiviral Innate Immunity; -Host Innate Immune Responses; Interaction with Host; Evade Host Antiviral Immunity -pathways: cGAS/STING-mediated DNA-sensing; Wnt Signaling; IFN pathway -gene_gene_interactions: US3 - β-Catenin; β-Catenin - US3 -gene_localizations: β-Catenin - Nuclear; US3 - Hyperphosphorylation -""" - -TEST_PROCESS = BiologicalProcess( - label="autophagosome assembly", - description="The formation of a double membrane-bounded structure, the autophagosome,\ - that occurs when a specialized membrane sac, called the isolation membrane,\ - starts to enclose a portion of the cytoplasm", - subclass_of="GO:0022607", - outputs=["GO:0005776"], -) - -DIRECT_PARSE = { - "genes": ["β-Catenin", "cGAS", "STING", "US3", "IFN", "ISG"], - "gene_organisms": [ - ("β-Catenin", "host"), - ("cGAS", "host"), - ("STING", "host"), - ("US3", "HSV-1"), - ("IFN", "host"), - ("ISG", "host"), - ], -} - - -class TestCore(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.ke = create_engine(TEMPLATE, SPIRESEngine) - - def test_setup(self): - """Tests template and module is loaded.""" - ke = self.ke - pyc = ke.template_pyclass - print(pyc) - obj = pyc(genes=["a"], gene_organisms=[{"gene": "a", "organism": "b"}]) - print(yaml.dump(obj.dict())) - self.assertEqual(obj.genes, ["a"]) - self.assertEqual(obj.gene_organisms[0].gene, "a") - self.assertEqual(obj.gene_organisms[0].organism, "b") - slot = ke.schemaview.induced_slot("genes", "GeneOrganismRelationship") - self.assertEqual(slot.name, "genes") - self.assertEqual(slot.multivalued, True) - self.assertEqual(slot.range, "Gene") - - def test_chunk_text(self): - """Test chunking.""" - text = "Title: foo. Abstract: Sentence 1. Sentence 2.\n Sentence 3. Sentence 4." - chunks = list(chunk_text(text)) - for chunk in chunks: - print(chunk) - self.assertEqual(len(chunks), 4) - self.assertEqual(chunks[0], "Title: foo") - self.assertEqual(chunks[1], "Title: foo. Abstract: Sentence 1") - self.assertEqual(chunks[2], "Title: foo. Abstract: Sentence 1. Sentence 2") - self.assertEqual(chunks[3], "Abstract: Sentence 1. Sentence 2. Sentence 3") - - def test_generalize(self): - """Tests generalization.""" - ke = SPIRESEngine("biological_process.BiologicalProcess") - ke.labelers = [get_implementation_from_shorthand("sqlite:obo:go")] - examples = [ - """ - label: mannose biosynthesis - description: The chemical reactions and pathways resulting - in the formation of mannose, the aldohexose manno-hexose, - the C-2 epimer of glucose. - synonyms: mannose anabolism - subclass_of: hexose biosynthesis - outputs: mannose - """, - """ - label: maltose biosynthesis - description: The chemical reactions and pathways - resulting in the formation of the - disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose) - subclass_of: disaccharide biosynthesis - outputs: maltose - """, - TEST_PROCESS, - ] - label = "beta-D-lyxofuranose biosynthesis" - ann = ke.generalize({"label": label}, examples) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - self.assertEqual(label, ann.label) - self.assertEqual(["CHEBI:151400"], ann.outputs) - - def test_serialize_example(self): - ke = SPIRESEngine("biological_process.BiologicalProcess") - ke.labelers = [get_implementation_from_shorthand("sqlite:obo:go")] - ser = ke.serialize_object(TEST_PROCESS) - # print(f"SERIALIZED={ser}") - self.assertIn("outputs: autophagosome", ser) - - def test_extract(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - ann = ke.extract_from_text(PAPER) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - results = ann.extracted_object - if not isinstance(results, GoCamAnnotations): - raise ValueError(f"Expected GoCamAnnotations, got {type(results)}") - self.assertIn("HGNC:2514", results.genes) - - def test_extract_with_stub(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - ann = ke.extract_from_text(PAPER, object={"pathways": ["GO:0140896"]}) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - results = ann.extracted_object - if not isinstance(results, GoCamAnnotations): - raise ValueError(f"Expected GoCamAnnotations, got {type(results)}") - self.assertIn("HGNC:2514", results.genes) - - def test_subextract(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - cls = ke.schemaview.get_class("GeneMolecularActivityRelationship") - ann = ke.extract_from_text("β-Catenin-Translocation", cls) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - self.assertEqual({"gene": "HGNC:2514", "molecular_activity": "Translocation"}, ann.dict()) - # try and fool it - ann = ke._extract_from_text_to_dict("foobaz", cls) - print(f"RESULTS={ann}") - self.assertIsNone(ann) - # print(yaml.dump(ann.dict())) - - def test_prompt(self): - """Tests prompt generation. - - Tests that the prompt can be derived from a prompt annotation, - or from description, if no such annotation present - """ - ke = self.ke - prompt = ke.get_completion_prompt() - self.assertIn( - "genes: ", - prompt, - "Expected to derived prompt from description of gene slot", - ) - self.assertIn( - "gene_organisms: ", - prompt, - "Expected to derived prompt from annotations of gene_organisms slot", - ) - - def test_parse_completion_payload(self): - """Tests parsing of textual payload from openai API. - - This involves two steps: - - - parsing the payload into a dict of slot values - - annotating the dict using OAK annotators - - We use a ready-made payload from the API, to avoid - invoking an API call - """ - ke = self.ke - ann = ke.parse_completion_payload(EXAMPLE_RESULTS) - print(f"PARSED={ann}") - print(yaml.dump(ann.dict())) - self.assertIn("HGNC:2514", ann.genes) - self.assertEqual(2, len(ann.pathways)) - - def test_parse_response_to_dict(self): - """Tests parsing of textual payload from openai API.""" - ke = self.ke - ann = ke._parse_response_to_dict(EXAMPLE_RESULTS) - print(f"PARSED={ann}") - print(yaml.dump(ann)) - self.assertIn("STING", ann["genes"]) - self.assertIn({"gene": "β-Catenin", "organism": "host"}, ann["gene_organisms"]) - # test resilience to missing internal separators - ann = ke._parse_response_to_dict("gene_organisms: a ; b ; c\ngenes: g") - self.assertEqual(ann["genes"], ["g"]) - self.assertEqual(["genes"], list(ann.keys())) - # test resilience to multiple internal separators - ann = ke._parse_response_to_dict("gene_organisms: a-b-c") - self.assertEqual(ann["gene_organisms"], [{"gene": "a", "organism": "b-c"}]) - - def test_parse_completion_payload_alt(self): - """Tests parsing of textual payload from openai API. - - This uses a variant of the output, sometimes OpenAI will - use ':' as separators instead of ' - '. - """ - ke = self.ke - ann = ke.parse_completion_payload(EXAMPLE_RESULTS_ALT) - print(f"PARSED={ann}") - print(dump_minimal_yaml(ann)) - - def test_ground_annotation_object(self): - """ - Tests grounding of annotation object. - - E.g. takes - - {'genes': ['β-Catenin', 'cGAS', ...]} - - And produces: - - {'genes': ['HGNC:2514', 'HGNC:21367', ... - """ - ke = self.ke - if not isinstance(ke, SPIRESEngine): - raise ValueError(f"Expected SPIRESEngine, got {type(ke)}") - annotated = ke.ground_annotation_object(DIRECT_PARSE) - print(dump_minimal_yaml(annotated)) - self.assertIn("HGNC:2514", annotated.genes) - expected = GeneOrganismRelationship(gene="HGNC:2514", organism="EFO:0000532") - self.assertIn(expected, annotated.gene_organisms) - - def test_normalize_named_entity(self): - ke = self.ke - normalize_cases = [ - ("β-Catenin", ClassDefinitionName(Gene.__name__), "HGNC:2514"), - ("nucleus", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ( - "transport", - ClassDefinitionName(GeneLocation.__name__), - "transport", - ), # not a location - ("perivascular macrophage", ClassDefinitionName(GeneLocation.__name__), "CL:0000881"), - ("perivascular macrophages", ClassDefinitionName(GeneLocation.__name__), "CL:0000881"), - ("blah blah (nucleus)", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ("nucleus (blah blah)", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ("NUCLEUS (blah blah)", ClassDefinitionName(GeneLocation.__name__), "GO:0005634"), - ] - for text, elt_name, expected in normalize_cases: - result = ke.normalize_named_entity(text, elt_name) - self.assertEqual(expected, result) - - def test_is_valid_identifier(self): - ke = self.ke - value_set_cases = [ - ("HGNC:2514", Gene, True), - ("CL:0000881", GeneLocation, True), - ("GO:0005634", GeneLocation, True), - ("HGNC:2514", GeneLocation, False), - ("GO:0005634", Gene, False), - ("GO:0006810", GeneLocation, False), # wrong hierarchy - ] - for curie, cls, is_valid in value_set_cases: - cls_def = ke.schemaview.get_class(cls.__name__) - result = ke.is_valid_identifier(curie, cls_def) - self.assertEqual( - result, is_valid, f"Expected validity of {curie} for {cls} to be {is_valid}" - ) - - def test_custom_dictionary(self): - ke = create_engine(TEMPLATE, SPIRESEngine) - ke.load_dictionary( - [ - {"synonym": "TING", "id": "HGNC:test1"}, - {"synonym": "sting", "id": "HGNC:test2"}, - {"synonym": "Cat", "id": "HGNC:test3"}, - ] - ) - if not isinstance(ke, SPIRESEngine): - raise ValueError(f"Expected TextModelKnowledgeEngine, got {type(ke)}") - annotated = ke.ground_annotation_object(DIRECT_PARSE) - print(dump_minimal_yaml(annotated)) - self.assertIn("HGNC:test2", annotated.genes) - self.assertNotIn("HGNC:test1", annotated.genes, "longer synonyms should take priority") - self.assertNotIn( - "HGNC:test3", - annotated.genes, - "number of overlapping characters should be beneath threshold", - ) - - def test_mapping(self): - """Tests mapping of annotation object to OAK model.""" - ke = self.ke - cases = [ - ( - "uberon", - [ - "pinky", - "brain", - "cerebellum", - "feet", - "epithelia", - "skin", - "hair", - "lungs", - "pancreatic", - "nerves", - "nostrils", - ], - ), - ( - "go", - [ - "Wnt signaling", - "apoptosis", - "lactase", - "positive regulation of alpha-glucoside transport", - "development of lungs", - ], - ), - ] - for ontology, terms in cases: - ann = ke.map_terms(terms, ontology) - print(yaml.dump(ann)) - - def test_extract_from_pubmed(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - pmc = PubmedClient() - text = pmc.text("PMID:27929086") - print(text) - ann = ke.extract_from_text(PAPER) - print(f"RESULTS={ann}") - print(yaml.dump(ann.dict())) - - def test_merge(self): - bp1 = BiologicalProcess( - label="bp", - description="d1", - synonyms=["s1a", "s1b", "shared"], - inputs=["c1", "c2"], - ) - bp2 = BiologicalProcess( - label="bp", - description="d2", - synonyms=["s2a", "s2b", "shared"], - outputs=["c3", "c4"], - ) - r1 = ExtractionResult(extracted_object=bp1) - r2 = ExtractionResult(extracted_object=bp2) - bp = self.ke.merge_resultsets([r1, r2]).extracted_object - print(yaml.dump(bp.dict())) - self.assertEqual("bp", bp.label) - self.assertEqual("d2", bp.description) - self.assertCountEqual(["s1a", "s1b", "s2a", "s2b", "shared"], bp.synonyms) - self.assertEqual(5, len(bp.synonyms), "Expected 5 distinct synonyms") - self.assertCountEqual(["c1", "c2", "c3", "c4"], bp.inputs + bp.outputs) - self.assertCountEqual(["c1", "c2"], bp.inputs) - self.assertCountEqual(["c3", "c4"], bp.outputs) - - def test_merge_with_pmids(self): - """Tests end to end knowledge extraction.""" - ke = self.ke - pmids = ["32716108", "27929086"] - pmc = PubmedClient() - rsets = [] - for pmid in pmids: - text = pmc.text(f"PMID:{pmid}") - rsets.append(ke.extract_from_text(text)) - print(f"Merging {len(rsets)} results") - merged = ke.merge_resultsets(rsets) - print(yaml.dump(merged.dict())) diff --git a/tests/output/README.md b/tests/output/README.md deleted file mode 100644 index 4460bf088..000000000 --- a/tests/output/README.md +++ /dev/null @@ -1 +0,0 @@ -Test results here diff --git a/tests/output/carbohydrate-metabolism.hallucinated.halo.yaml b/tests/output/carbohydrate-metabolism.hallucinated.halo.yaml deleted file mode 100644 index 42d9a24f5..000000000 --- a/tests/output/carbohydrate-metabolism.hallucinated.halo.yaml +++ /dev/null @@ -1,993 +0,0 @@ -elements: -- name: Fat-solubleVitaminMetabolicProcess - description: The chemical reactions and pathways involving of any of a diverse group - of vitamins that are soluble in organic solvents and relatively insoluble in water. - synonyms: - - fat-soluble vitamin metabolism - subclass_of: - - VitaminMetabolicProcess - subtypes: - - Fat-solubleVitaminCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some SubstanceWithFat-solubleVitamin(role)Role -- name: LipidMetabolicProcess - description: The chemical reactions and pathways involving lipids, compounds soluble - in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty - acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols - and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and - sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. - synonyms: - - lipid metabolism - subclass_of: - - PrimaryMetabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - SteroidMetabolicProcess - - LipidBiosyntheticProcess - - LipidCatabolicProcess - - CellularLipidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Lipid -- name: OlefinicCompoundMetabolicProcess - description: The chemical reactions and pathways involving an olefinic compound, - any compound which contains a carbon-carbon double bond (aka C=C). - synonyms: - - alkene substituted compound metabolic process - - alkene substituted compound metabolism - subclass_of: - - OrganicSubstanceMetabolicProcess - subtypes: - - CortisolMetabolicProcess - - OlefinicCompoundBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some OlefinicCompound -- name: TertiaryAlcoholMetabolicProcess - description: The chemical reactions and pathways involving tertiary alcohol. - synonyms: - - tertiary alcohol metabolism - subclass_of: - - AlcoholMetabolicProcess - subtypes: - - CortisolMetabolicProcess - - TertiaryAlcoholBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some TertiaryAlcohol -- name: OrganicSubstanceBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of an - organic substance, any molecular entity containing carbon. - synonyms: - - organic molecular entity anabolism - - organic molecular entity biosynthesis - - organic molecular entity biosynthetic process - - organic molecular entity formation - - organic molecular entity synthesis - - organic substance anabolism - - organic substance biosynthesis - - organic substance formation - - organic substance synthesis - subclass_of: - - BiosyntheticProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - LipidBiosyntheticProcess - - KetoneBiosyntheticProcess - - OlefinicCompoundBiosyntheticProcess - - OrganicCyclicCompoundBiosyntheticProcess - - OrganicHydroxyCompoundBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OrganicMolecularEntity -- name: HormoneMetabolicProcess - description: The chemical reactions and pathways involving any hormone, naturally - occurring substances secreted by specialized cells that affects the metabolism - or behavior of other cells possessing functional receptors for the hormone. - synonyms: - - hormone metabolism - - cellular hormone metabolic process - subclass_of: - - MetabolicProcess - - RegulationOfHormoneLevels - subtypes: - - RetinoicAcidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some SubstanceWithHormoneRole -- name: OrganicSubstanceCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of an - organic substance, any molecular entity containing carbon. - synonyms: - - organic molecular entity breakdown - - organic molecular entity catabolic process - - organic molecular entity catabolism - - organic molecular entity degradation - - organic substance breakdown - - organic substance catabolism - - organic substance degradation - subclass_of: - - CatabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - LipidCatabolicProcess - - OrganicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some OrganicMolecularEntity -- name: AlcoholBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of alcohols, - any of a class of compounds containing one or more hydroxyl groups attached to - a saturated carbon atom. - synonyms: - - alcohol anabolism - - alcohol biosynthesis - - alcohol formation - - alcohol synthesis - subclass_of: - - AlcoholMetabolicProcess - - SmallMoleculeBiosyntheticProcess - - OrganicHydroxyCompoundBiosyntheticProcess - subtypes: - - PrimaryAlcoholBiosyntheticProcess - - TertiaryAlcoholBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Alcohol -- name: CellularKetoneMetabolicProcess - description: The chemical reactions and pathways involving any of a class of organic - compounds that contain the carbonyl group, CO, and in which the carbonyl group - is bonded only to carbon atoms, as carried out by individual cells. The general - formula for a ketone is RCOR, where R and R are alkyl or aryl groups. - synonyms: - - ketone metabolism - subclass_of: - - CellularMetabolicProcess - - SmallMoleculeMetabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - CortisolMetabolicProcess - - KetoneBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some Ketone -- name: CarboxylicAcidMetabolicProcess - description: The chemical reactions and pathways involving carboxylic acids, any - organic acid containing one or more carboxyl (COOH) groups or anions (COO-). - synonyms: - - carboxylic acid metabolism - subclass_of: - - OxoacidMetabolicProcess - subtypes: - - MonocarboxylicAcidMetabolicProcess - - CarboxylicAcidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some CarboxylicAcidAnion -- name: GlucocorticoidMetabolicProcess - description: The chemical reactions and pathways involving glucocorticoids, hormonal - C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily - on carbohydrate and protein metabolism, and have anti-inflammatory effects. - synonyms: - - glucocorticoid metabolism - - glucocorticosteroid metabolic process - - glucocorticosteroid metabolism - subclass_of: - - SteroidMetabolicProcess - subtypes: - - GlucocorticoidBiosyntheticProcess - - CortisolMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Glucocorticoid -- name: CellularLipidMetabolicProcess - description: The chemical reactions and pathways involving lipids, as carried out - by individual cells. - synonyms: - - cellular lipid metabolism - subclass_of: - - LipidMetabolicProcess - - CellularMetabolicProcess - subtypes: - - IsoprenoidMetabolicProcess - - CellularLipidCatabolicProcess -- name: OlefinicCompoundBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of an - olefinic compound, any compound which contains a carbon-carbon double bond (aka - C=C). - synonyms: - - alkene substituted compound anabolic process - - alkene substituted compound anabolism - - alkene substituted compound biosynthesis - - alkene substituted compound biosynthetic process - - alkene substituted compound synthesis - subclass_of: - - OlefinicCompoundMetabolicProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OlefinicCompound -- name: CellularProcess - description: Any process that is carried out at the cellular level, but not necessarily - restricted to a single cell. For example, cell communication occurs among more - than one cell, but occurs at the cellular level. - synonyms: - - cell physiology - - cellular physiological process - - cell growth and/or maintenance - - single-organism cellular process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: LipidBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of lipids, - compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - synonyms: - - lipid anabolism - - lipid biosynthesis - - lipid formation - - lipid synthesis - - lipogenesis - subclass_of: - - LipidMetabolicProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - SteroidBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Lipid -- name: CellularBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of substances, - carried out by individual cells. - synonyms: - - cellular anabolism - - cellular biosynthesis - - cellular formation - - cellular synthesis - subclass_of: - - BiosyntheticProcess - - CellularMetabolicProcess - subtypes: - - KetoneBiosyntheticProcess -- name: SteroidMetabolicProcess - description: The chemical reactions and pathways involving steroids, compounds with - a 1,2,cyclopentanoperhydrophenanthrene nucleus. - synonyms: - - steroid metabolism - subclass_of: - - LipidMetabolicProcess - - OrganicCyclicCompoundMetabolicProcess - subtypes: - - SteroidBiosyntheticProcess - - GlucocorticoidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Steroid -- name: PrimaryAlcoholBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of primary - alcohols. A primary alcohol is any alcohol in which a hydroxy group, -OH, is attached - to a saturated carbon atom which has either three hydrogen atoms attached to it - or only one other carbon atom and two hydrogen atoms attached to it. - synonyms: - - monohydric alcohol biosynthetic process - - primary alcohol anabolism - - primary alcohol biosynthesis - - primary alcohol formation - - primary alcohol synthesis - subclass_of: - - PrimaryAlcoholMetabolicProcess - - AlcoholBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some PrimaryAlcohol -- name: KetoneBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of ketones, - a class of organic compounds that contain the carbonyl group, CO, and in which - the carbonyl group is bonded only to carbon atoms. The general formula for a ketone - is RCOR, where R and R are alkyl or aryl groups. - synonyms: - - ketone anabolism - - ketone biosynthesis - - ketone formation - - ketone synthesis - subclass_of: - - CellularKetoneMetabolicProcess - - CellularBiosyntheticProcess - - SmallMoleculeBiosyntheticProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Ketone -- name: Occurrent - description: An entity that has temporal parts and that happens, unfolds or develops - through time. - subtypes: - - Process -- name: CortisolBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of cortisol, - the steroid hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is - synthesized from cholesterol in the adrenal gland and controls carbohydrate, fat - and protein metabolism and has anti-inflammatory properties. - synonyms: - - cortisol biosynthesis - - cortisol formation - - cortisol synthesis - - cortisol anabolism - subclass_of: - - GlucocorticoidBiosyntheticProcess - - PrimaryAlcoholBiosyntheticProcess - - CortisolMetabolicProcess - - KetoneBiosyntheticProcess - - OlefinicCompoundBiosyntheticProcess - - TertiaryAlcoholBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Cortisol -- name: OrganicSubstanceMetabolicProcess - description: The chemical reactions and pathways involving an organic substance, - any molecular entity containing carbon. - synonyms: - - organic molecular entity metabolic process - - organic molecular entity metabolism - - organic substance metabolism - subclass_of: - - MetabolicProcess - subtypes: - - OrganicAcidMetabolicProcess - - LipidMetabolicProcess - - CellularKetoneMetabolicProcess - - OlefinicCompoundMetabolicProcess - - OrganicCyclicCompoundMetabolicProcess - - OrganicSubstanceCatabolicProcess - - OrganicSubstanceBiosyntheticProcess - - OrganicHydroxyCompoundMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicMolecularEntity -- name: OrganicCyclicCompoundBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of organic - cyclic compound. - synonyms: - - organic cyclic compound anabolism - - organic cyclic compound biosynthesis - - organic cyclic compound formation - - organic cyclic compound synthesis - subclass_of: - - OrganicCyclicCompoundMetabolicProcess - - OrganicSubstanceBiosyntheticProcess - subtypes: - - SteroidBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OrganicCyclicCompound -- name: OrganicHydroxyCompoundMetabolicProcess - description: The chemical reactions and pathways involving organic hydroxy compound. - synonyms: - - organic hydroxy compound metabolism - subclass_of: - - OrganicSubstanceMetabolicProcess - subtypes: - - AlcoholMetabolicProcess - - OrganicHydroxyCompoundBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicHydroxyCompound -- name: OrganicHydroxyCompoundBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of organic - hydroxy compound. - synonyms: - - organic hydroxy compound anabolism - - organic hydroxy compound biosynthesis - - organic hydroxy compound formation - - organic hydroxy compound synthesis - subclass_of: - - OrganicSubstanceBiosyntheticProcess - - OrganicHydroxyCompoundMetabolicProcess - subtypes: - - AlcoholBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some OrganicHydroxyCompound -- name: IsoprenoidMetabolicProcess - description: The chemical reactions and pathways involving isoprenoid compounds, - isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked - isoprene (3-methyl-2-butenylene) residues. - synonyms: - - isoprenoid metabolism - - polyisoprenoid metabolic process - - polyisoprenoid metabolism - - polyterpene metabolic process - - polyterpene metabolism - subclass_of: - - CellularLipidMetabolicProcess - subtypes: - - TerpenoidMetabolicProcess - - IsoprenoidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Isoprenoid -- name: TerpenoidMetabolicProcess - description: The chemical reactions and pathways involving terpenoids, any member - of a class of compounds characterized by an isoprenoid chemical structure and - including derivatives with various functional groups. - synonyms: - - terpenoid metabolism - subclass_of: - - IsoprenoidMetabolicProcess - subtypes: - - DiterpenoidMetabolicProcess - - TerpenoidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Terpenoid -- name: IsoprenoidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of an - isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing - or derived from linked isoprene (3-methyl-2-butenylene) residues. - synonyms: - - isoprenoid breakdown - - isoprenoid catabolism - - isoprenoid degradation - - polyisoprenoid breakdown - - polyisoprenoid catabolic process - - polyisoprenoid catabolism - - polyisoprenoid degradation - - polyterpene catabolic process - - polyterpene catabolism - subclass_of: - - IsoprenoidMetabolicProcess - - CellularLipidCatabolicProcess - subtypes: - - TerpenoidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Isoprenoid -- name: CatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of substances, - including the breakdown of carbon compounds with the liberation of energy for - use by the cell or organism. - synonyms: - - breakdown - - catabolism - - degradation - - multicellular organismal catabolic process - - single-organism catabolic process - subclass_of: - - MetabolicProcess - subtypes: - - CellularCatabolicProcess - - SmallMoleculeCatabolicProcess - - OrganicSubstanceCatabolicProcess -- name: DiterpenoidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of diterpenoid - compounds, terpenoids with four isoprene units. - synonyms: - - diterpenoid breakdown - - diterpenoid catabolism - - diterpenoid degradation - - diterpene catabolic process - - diterpene catabolism - subclass_of: - - DiterpenoidMetabolicProcess - - TerpenoidCatabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Diterpenoid -- name: LipidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of lipids, - compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. - synonyms: - - lipid breakdown - - lipid catabolism - - lipid degradation - - lipolysis - - multicellular organism lipid catabolic process - - multicellular organismal lipid catabolic process - subclass_of: - - LipidMetabolicProcess - - OrganicSubstanceCatabolicProcess - subtypes: - - CellularLipidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Lipid -- name: Fat-solubleVitaminCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of any - of a diverse group of vitamins that are soluble in organic solvents and relatively - insoluble in water. - synonyms: - - fat-soluble vitamin breakdown - - fat-soluble vitamin catabolism - - fat-soluble vitamin degradation - subclass_of: - - Fat-solubleVitaminMetabolicProcess - - VitaminCatabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some SubstanceWithFat-solubleVitamin(role)Role -- name: RetinoicAcidMetabolicProcess - description: The chemical reactions and pathways involving retinoic acid, one of - the three components that makes up vitamin A. - synonyms: - - retinoic acid metabolism - - vitamin A1 acid metabolic process - - vitamin A1 acid metabolism - subclass_of: - - RetinoidMetabolicProcess - - MonocarboxylicAcidMetabolicProcess - - HormoneMetabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Retinoate -- name: OxoacidMetabolicProcess - description: The chemical reactions and pathways involving any oxoacid; an oxoacid - is a compound which contains oxygen, at least one other element, and at least - one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive - hydrogen ion(s) (hydrons). - synonyms: - - keto acid metabolic process - - keto acid metabolism - - ketoacid metabolic process - - ketoacid metabolism - - oxo acid metabolic process - - oxo acid metabolism - - oxoacid metabolism - subclass_of: - - OrganicAcidMetabolicProcess - subtypes: - - CarboxylicAcidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Oxoanion -- name: MetabolicProcess - description: The chemical reactions and pathways, including anabolism and catabolism, - by which living organisms transform chemical substances. Metabolic processes typically - transform small molecules, but also include macromolecular processes such as DNA - repair and replication, and protein synthesis and degradation. - synonyms: - - metabolism - - metabolic process resulting in cell growth - - metabolism resulting in cell growth - - multicellular organism metabolic process - - single-organism metabolic process - subclass_of: - - BiologicalProcess - subtypes: - - CatabolicProcess - - BiosyntheticProcess - - HormoneMetabolicProcess - - CellularMetabolicProcess - - PrimaryMetabolicProcess - - SmallMoleculeMetabolicProcess - - OrganicSubstanceMetabolicProcess -- name: CarboxylicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of carboxylic - acids, any organic acid containing one or more carboxyl (-COOH) groups. - synonyms: - - carboxylic acid breakdown - - carboxylic acid catabolism - - carboxylic acid degradation - subclass_of: - - OrganicAcidCatabolicProcess - - CarboxylicAcidMetabolicProcess - subtypes: - - MonocarboxylicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some CarboxylicAcidAnion -- name: SteroidHormoneBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of any - steroid hormone, naturally occurring substances secreted by specialized cells - that affects the metabolism or behavior of other cells possessing functional receptors - for the hormone. - subclass_of: - - SteroidBiosyntheticProcess - subtypes: - - GlucocorticoidBiosyntheticProcess - equivalent_to: SteroidBiosyntheticProcess and has output some SteroidHormone -- name: GlucocorticoidBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of glucocorticoids, - hormonal C21 corticosteroids synthesized from cholesterol. - synonyms: - - glucocorticoid anabolism - - glucocorticoid biosynthesis - - glucocorticoid formation - - glucocorticoid synthesis - subclass_of: - - GlucocorticoidMetabolicProcess - - SteroidHormoneBiosyntheticProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Glucocorticoid -- name: TertiaryAlcoholBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of tertiary - alcohol. - synonyms: - - tertiary alcohol anabolism - - tertiary alcohol biosynthesis - - tertiary alcohol formation - - tertiary alcohol synthesis - subclass_of: - - AlcoholBiosyntheticProcess - - TertiaryAlcoholMetabolicProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some TertiaryAlcohol -- name: VitaminMetabolicProcess - description: The chemical reactions and pathways involving vitamins. Vitamin is - a general term for a number of unrelated organic substances that occur in many - foods in small amounts and that are necessary in trace amounts for the normal - metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble - and usually serve as components of coenzyme systems. - synonyms: - - vitamin metabolism - subclass_of: - - SmallMoleculeMetabolicProcess - subtypes: - - Fat-solubleVitaminMetabolicProcess - - VitaminCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some SubstanceWithVitamin(role)Role -- name: SmallMoleculeBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of small - molecules, any low molecular weight, monomeric, non-encoded molecule. - synonyms: - - small molecule biosynthesis - subclass_of: - - BiosyntheticProcess - - SmallMoleculeMetabolicProcess - subtypes: - - KetoneBiosyntheticProcess - - AlcoholBiosyntheticProcess -- name: OrganicCyclicCompoundMetabolicProcess - description: The chemical reactions and pathways involving organic cyclic compound. - synonyms: - - organic cyclic compound metabolism - subclass_of: - - OrganicSubstanceMetabolicProcess - subtypes: - - SteroidMetabolicProcess - - OrganicCyclicCompoundBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicCyclicCompound -- name: OrganicAcidMetabolicProcess - description: The chemical reactions and pathways involving organic acids, any acidic - compound containing carbon in covalent linkage. - synonyms: - - organic acid metabolism - subclass_of: - - CellularMetabolicProcess - - SmallMoleculeMetabolicProcess - - OrganicSubstanceMetabolicProcess - subtypes: - - OrganicAcidCatabolicProcess - - OxoacidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some OrganicAcid -- name: OrganicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of organic - acids, any acidic compound containing carbon in covalent linkage. - synonyms: - - organic acid breakdown - - organic acid catabolism - - organic acid degradation - subclass_of: - - OrganicAcidMetabolicProcess - - CellularCatabolicProcess - - SmallMoleculeCatabolicProcess - - OrganicSubstanceCatabolicProcess - subtypes: - - CarboxylicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some OrganicAcid -- name: SmallMoleculeCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of small - molecules, any low molecular weight, monomeric, non-encoded molecule. - synonyms: - - small molecule catabolism - subclass_of: - - CatabolicProcess - - SmallMoleculeMetabolicProcess - subtypes: - - VitaminCatabolicProcess - - OrganicAcidCatabolicProcess -- name: RegulationOfBiologicalQuality - description: Any process that modulates a qualitative or quantitative trait of a - biological quality. A biological quality is a measurable attribute of an organism - or part of an organism, such as size, mass, shape, color, etc. - synonyms: - - regulation of biological attribute - - regulation of biological characteristic - subclass_of: - - BiologicalRegulation - subtypes: - - RegulationOfHormoneLevels - equivalent_to: BiologicalRegulation and regulates characteristic some BiologicalAttribute -- name: CellularLipidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of lipids, - as carried out by individual cells. - synonyms: - - cellular lipid breakdown - - cellular lipid catabolism - - cellular lipid degradation - subclass_of: - - LipidCatabolicProcess - - CellularCatabolicProcess - - CellularLipidMetabolicProcess - subtypes: - - IsoprenoidCatabolicProcess -- name: CortisolMetabolicProcess - description: The chemical reactions and pathways involving cortisol, the steroid - hormone 11-beta-17,21-trihydroxypregn-4-ene-3,20-dione. Cortisol is synthesized - from cholesterol in the adrenal gland and controls carbohydrate, fat and protein - metabolism and has anti-inflammatory properties. - synonyms: - - cortisol metabolism - subclass_of: - - GlucocorticoidMetabolicProcess - - PrimaryAlcoholMetabolicProcess - - CellularKetoneMetabolicProcess - - OlefinicCompoundMetabolicProcess - - TertiaryAlcoholMetabolicProcess - subtypes: - - CortisolBiosyntheticProcess - equivalent_to: MetabolicProcess and has primary input or output some Cortisol -- name: BiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of substances; - typically the energy-requiring part of metabolism in which simpler substances - are transformed into more complex ones. - synonyms: - - formation - - anabolism - - biosynthesis - - synthesis - - multicellular organismal biosynthetic process - - single-organism biosynthetic process - subclass_of: - - MetabolicProcess - subtypes: - - CellularBiosyntheticProcess - - SmallMoleculeBiosyntheticProcess - - OrganicSubstanceBiosyntheticProcess -- name: SteroidBiosyntheticProcess - description: The chemical reactions and pathways resulting in the formation of steroids, - compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo - formation and steroid interconversion by modification. - synonyms: - - steroid anabolism - - steroid biosynthesis - - steroid formation - - steroid synthesis - - steroidogenesis - subclass_of: - - SteroidMetabolicProcess - - LipidBiosyntheticProcess - - OrganicCyclicCompoundBiosyntheticProcess - subtypes: - - SteroidHormoneBiosyntheticProcess - equivalent_to: BiosyntheticProcess and has primary output some Steroid -- name: BiologicalProcess - description: A biological process represents a specific objective that the organism - is genetically programmed to achieve. Biological processes are often described - by their outcome or ending state, e.g., the biological process of cell division - results in the creation of two daughter cells (a divided cell) from a single parent - cell. A biological process is accomplished by a particular set of molecular functions - carried out by specific gene products (or macromolecular complexes), often in - a highly regulated manner and in a particular temporal sequence. - synonyms: - - biological process - - physiological process - - single organism process - - single-organism process - subclass_of: - - Process - subtypes: - - MetabolicProcess - - CellularProcess - - BiologicalRegulation -- name: RetinoidMetabolicProcess - description: The chemical reactions and pathways involving retinoids, any member - of a class of isoprenoids that contain or are derived from four prenyl groups - linked head-to-tail. Retinoids include retinol and retinal and structurally similar - natural derivatives or synthetic compounds, but need not have vitamin A activity. - synonyms: - - retinoid metabolism - subclass_of: - - DiterpenoidMetabolicProcess - subtypes: - - RetinoicAcidMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Retinoid -- name: DiterpenoidMetabolicProcess - description: The chemical reactions and pathways involving diterpenoid compounds, - terpenoids with four isoprene units. - synonyms: - - diterpenoid metabolism - - diterpene metabolic process - - diterpene metabolism - subclass_of: - - TerpenoidMetabolicProcess - subtypes: - - RetinoidMetabolicProcess - - DiterpenoidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Diterpenoid -- name: AlcoholMetabolicProcess - description: The chemical reactions and pathways involving alcohols, any of a class - of compounds containing one or more hydroxyl groups attached to a saturated carbon - atom. - synonyms: - - alcohol metabolism - subclass_of: - - SmallMoleculeMetabolicProcess - - OrganicHydroxyCompoundMetabolicProcess - subtypes: - - PrimaryAlcoholMetabolicProcess - - AlcoholBiosyntheticProcess - - TertiaryAlcoholMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Alcohol -- name: MonocarboxylicAcidMetabolicProcess - description: The chemical reactions and pathways involving monocarboxylic acids, - any organic acid containing one carboxyl (COOH) group or anion (COO-). - synonyms: - - monocarboxylate metabolic process - - monocarboxylic acid metabolism - subclass_of: - - CarboxylicAcidMetabolicProcess - subtypes: - - RetinoicAcidMetabolicProcess - - MonocarboxylicAcidCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some MonocarboxylicAcidAnion -- name: BiologicalRegulation - description: Any process that modulates a measurable attribute of any biological - process, quality or function. - synonyms: - - regulation - subclass_of: - - BiologicalProcess - subtypes: - - RegulationOfBiologicalQuality -- name: CellularCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of substances, - carried out by individual cells. - synonyms: - - cellular breakdown - - cellular catabolism - - cellular degradation - subclass_of: - - CatabolicProcess - - CellularMetabolicProcess - subtypes: - - VitaminCatabolicProcess - - OrganicAcidCatabolicProcess - - CellularLipidCatabolicProcess -- name: Process - description: An occurrent that has temporal proper parts and for some time t, p - s-depends_on some material entity at t. - subclass_of: - - Occurrent - subtypes: - - BiologicalProcess -- name: PrimaryAlcoholMetabolicProcess - description: The chemical reactions and pathways involving primary alcohols. A primary - alcohol is any alcohol in which a hydroxy group, -OH, is attached to a saturated - carbon atom which has either three hydrogen atoms attached to it or only one other - carbon atom and two hydrogen atoms attached to it. - synonyms: - - monohydric alcohol metabolic process - - primary alcohol metabolism - subclass_of: - - AlcoholMetabolicProcess - subtypes: - - PrimaryAlcoholBiosyntheticProcess - - CortisolMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some PrimaryAlcohol -- name: TerpenoidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of terpenoids, - any member of a class of compounds characterized by an isoprenoid chemical structure. - synonyms: - - terpenoid breakdown - - terpenoid catabolism - - terpenoid degradation - subclass_of: - - TerpenoidMetabolicProcess - - IsoprenoidCatabolicProcess - subtypes: - - DiterpenoidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Terpenoid -- name: MonocarboxylicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of monocarboxylic - acids, any organic acid containing one carboxyl (-COOH) group. - subclass_of: - - MonocarboxylicAcidMetabolicProcess - - CarboxylicAcidCatabolicProcess - subtypes: - - RetinoicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some MonocarboxylicAcidAnion -- name: SmallMoleculeMetabolicProcess - description: The chemical reactions and pathways involving small molecules, any - low molecular weight, monomeric, non-encoded molecule. - synonyms: - - small molecule metabolism - subclass_of: - - MetabolicProcess - subtypes: - - AlcoholMetabolicProcess - - OrganicAcidMetabolicProcess - - VitaminMetabolicProcess - - CellularKetoneMetabolicProcess - - SmallMoleculeCatabolicProcess - - SmallMoleculeBiosyntheticProcess -- name: RegulationOfHormoneLevels - description: Any process that modulates the levels of hormone within an organism - or a tissue. A hormone is any substance formed in very small amounts in one specialized - organ or group of cells and carried (sometimes in the bloodstream) to another - organ or group of cells in the same organism, upon which it has a specific regulatory - action. - subclass_of: - - RegulationOfBiologicalQuality - subtypes: - - HormoneMetabolicProcess - equivalent_to: BiologicalRegulation and regulates characteristic some HormoneLevels -- name: VitaminCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of a - vitamin, one of a number of unrelated organic substances that occur in many foods - in small amounts and that are necessary in trace amounts for the normal metabolic - functioning of the body. - synonyms: - - vitamin breakdown - - vitamin catabolism - - vitamin degradation - subclass_of: - - VitaminMetabolicProcess - - CellularCatabolicProcess - - SmallMoleculeCatabolicProcess - subtypes: - - Fat-solubleVitaminCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some SubstanceWithVitamin(role)Role -- name: PrimaryMetabolicProcess - description: The chemical reactions and pathways involving those compounds which - are formed as a part of the normal anabolic and catabolic processes. These processes - take place in most, if not all, cells of the organism. - synonyms: - - primary metabolism - subclass_of: - - MetabolicProcess - subtypes: - - LipidMetabolicProcess -- name: CellularMetabolicProcess - description: The chemical reactions and pathways by which individual cells transform - chemical substances. - synonyms: - - cellular metabolism - - intermediary metabolism - subclass_of: - - MetabolicProcess - - CellularProcess - subtypes: - - OrganicAcidMetabolicProcess - - CellularKetoneMetabolicProcess - - CellularCatabolicProcess - - CellularBiosyntheticProcess - - CellularLipidMetabolicProcess -- name: RetinoicAcidCatabolicProcess - description: The chemical reactions and pathways resulting in the breakdown of retinoic - acid, one of the three components that makes up vitamin A. - synonyms: - - retinoic acid breakdown - - retinoic acid catabolism - - retinoic acid degradation - - vitamin A1 acid catabolic process - subclass_of: - - DiterpenoidCatabolicProcess - - Fat-solubleVitaminCatabolicProcess - - RetinoicAcidMetabolicProcess - - MonocarboxylicAcidCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Retinoate -- name: KetoaldopentoseBiosyntheticProcess - context: metabolism - description: The chemical reactions and pathways resulting in the formation of ketoaldopentose. -- name: IsomaltotrioseMetabolicProcess - context: metabolism - description: The chemical reactions and pathways involving any isomaltotriose, an - isomeric mixture of 3-alpha, 6-alpha-disaccharide containing an alpha prenyle - group. - synonyms: - - isomaltotriose metabolism - categories: - - metabolism - subtypes: - - IsomaltotrioseBiosyntheticProcess - - IsomaltotrioseCatabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some Isomaltotriose -- name: IsomaltotrioseBiosyntheticProcess - context: metabolism - description: The chemical reactions and pathways resulting in the formation of any - isomaltotriose, an isomeric mixture of 3-alpha, 6-alpha-disaccharide containing - an alpha prenyle group. - synonyms: - - isomaltotriose biosynthesis - - isomaltotriose formation - - isomaltotriose synthesis - - isomaltotriose anabolism - subclass_of: - - AcylglucosideBiosyntheticProcess - - IsomaltotrioseMetabolicProcess - equivalent_to: BiosyntheticProcess and has primary output some Isomaltotriose -- name: IsomaltotrioseCatabolicProcess - context: metabolism - description: The chemical reactions and pathways resulting in the breakdown of an - isomaltotriose, an isomeric mixture of 3-alpha, 6-alpha-disaccharide containing - an alpha prenyle group. - synonyms: - - isomaltotriose breakdown - - isomaltotriose degradation - subclass_of: - - IsomaltotrioseMetabolicProcess - part_of: - - AcylglucosideCatabolicProcess - equivalent_to: CatabolicProcess and has primary input some Isomaltotriose -- name: AcylglucosideBiosyntheticProcess - context: metabolism - synonyms: - - acylglucoside anabolism - - acylglucoside biosynthesis - - acylglucoside biosynthetic process - - acylglucoside formation - - acyl glucoside biosynthetic process - - acyl glucoside formation - - acyl glucoside biosynthesis - - acyl glucoside synthesis - - acylglucoside synthesis - categories: - - AcylglucosideBiosyntheticProcess - - anabolic_process - - organic_substance_biosynthetic_process diff --git a/tests/output/drug-DB00316-moa.pickle b/tests/output/drug-DB00316-moa.pickle deleted file mode 100644 index 4d80fc6dc..000000000 Binary files a/tests/output/drug-DB00316-moa.pickle and /dev/null differ diff --git a/tests/output/drug-DB00316-moa.yaml b/tests/output/drug-DB00316-moa.yaml deleted file mode 100644 index 2be88f394..000000000 --- a/tests/output/drug-DB00316-moa.yaml +++ /dev/null @@ -1,106 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/drug-DB00316-moa.txt -input_text: 'According to its FDA labeling, acetaminophen''s exact mechanism of action - has not been fully establishedLabel - despite this, it is often categorized alongside - NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the - cyclooxygenase (COX) pathways.14 It is thought to exert central actions which ultimately - lead to the alleviation of pain symptoms.14 - - - One theory is that acetaminophen increases the pain threshold by inhibiting two - isoforms of cyclooxygenase, COX-1 and COX-2, which are involved in prostaglandin - (PG) synthesis. Prostaglandins are responsible for eliciting pain sensations.13 - Acetaminophen does not inhibit cyclooxygenase in peripheral tissues and, therefore, - has no peripheral anti-inflammatory effects. Though acetylsalicylic acid (aspirin) - is an irreversible inhibitor of COX and directly blocks the active site of this - enzyme, studies have shown that acetaminophen (paracetamol) blocks COX indirectly.24 - Studies also suggest that acetaminophen selectively blocks a variant type of the - COX enzyme that is unique from the known variants COX-1 and COX-2.6 This enzyme - has been referred to as COX-3. The antipyretic actions of acetaminophen are likely - attributed to direct action on heat-regulating centers in the brain, resulting in - peripheral vasodilation, sweating, and loss of body heat.24 The exact mechanism - of action of this drug is not fully understood at this time, but future research - may contribute to deeper knowledge' -raw_completion_output: 'Disease: Pain Symptoms; - - Drug: Acetaminophen; - - Mechanism_links: cyclooxygenase (COX)-pain sensations;13; COX-1-acetaminophen;14; - COX-2-acetaminophen;14; COX-3-acetaminophen;6; antipyretic-direct action on heat-regulating - centers;24' -prompt: 'Split the following piece of text into fields in the following format: - - - subject: - - predicate: - - object: - - - - Text: - - 24 - - - === - - - ' -extracted_object: - disease: AUTO:Pain%20Symptoms%3B - drug: AUTO:Acetaminophen%3B - mechanism_links: - - subject: MESH:D011451 - predicate: AUTO:-pain - object: MESH:D012677 - - subject: AUTO:COX-1 - predicate: AUTO:acetaminophen - object: AUTO:- - - subject: AUTO:14 - - subject: AUTO:COX-2 - predicate: - object: MESH:D000082 - - subject: AUTO:14 - - subject: AUTO:COX-3 - predicate: AUTO:acetaminophen - object: AUTO:- - - subject: MESH:D058633 - predicate: AUTO:direct%20action%20on - object: AUTO:heat-regulating%20centers - - subject: AUTO:24 -named_entities: -- id: AUTO:Pain%20Symptoms%3B - label: Pain Symptoms; -- id: AUTO:Acetaminophen%3B - label: Acetaminophen; -- id: MESH:D011451 - label: cyclooxygenase (COX) -- id: AUTO:-pain - label: -pain -- id: MESH:D012677 - label: sensations -- id: AUTO:COX-1 - label: COX-1 -- id: AUTO:acetaminophen - label: acetaminophen -- id: AUTO:- - label: '-' -- id: AUTO:14 - label: '14' -- id: AUTO:COX-2 - label: COX-2 -- id: - label: '-' -- id: MESH:D000082 - label: Acetaminophen -- id: AUTO:COX-3 - label: COX-3 -- id: MESH:D058633 - label: antipyretic -- id: AUTO:direct%20action%20on - label: direct action on -- id: AUTO:heat-regulating%20centers - label: heat-regulating centers -- id: AUTO:24 - label: '24' diff --git a/tests/output/drugmechdb-normalized.yaml.gz b/tests/output/drugmechdb-normalized.yaml.gz deleted file mode 100644 index e417300dc..000000000 Binary files a/tests/output/drugmechdb-normalized.yaml.gz and /dev/null differ diff --git a/tests/output/eds-output.html b/tests/output/eds-output.html deleted file mode 100644 index 5d622bf97..000000000 --- a/tests/output/eds-output.html +++ /dev/null @@ -1,573 +0,0 @@ -

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

-

Input

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

Results

-
-

disease

-Ehlers Danlos Syndrome MONDO:0020066 -

drugs

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

treatments

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

treatment_mechanisms

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

treatment_efficacies

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

YAML Object

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

Prompt

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

Completion

-
-
-Disease: Ehlers Danlos Syndrome
-Drugs: Ascorbic Acid (Vitamin C)
-Treatments: Preventative measures; Deep stiches; Superficial stiches; Ascorbic Acid (Vitamin C); Avoidance of heavy sports, lifting, and other strenuous efforts; Screening for hypertension and arterial disease; Non-invasive technology screening; Careful consideration of surgery for non-life threatening conditions; Monitoring during pregnancy; Physical therapy; Low-resistance exercise; Assistive devices; Comfortable writing utensils; Low-stress mattress; Pain management; Calcium and vitamin D; DEXA bone density scans; Routine eye exams; Protective bandages
-Treatment Mechanisms: Deep stiches*wound healing; Superficial stiches*scarring; Ascorbic Acid (Vitamin C)*bruising; Avoidance of heavy sports, lifting, and other strenuous efforts*prevention; Screening for hypertension and arterial disease*arterial screening; Non-invasive technology screening*screening; Careful consideration of surgery for non-life threatening conditions*prevention; Monitoring during pregnancy*screening; Physical therapy*musculoskeletal pain; Low-resistance exercise*musculoskeletal pain; Assistive devices*musculoskeletal pain; Comfortable writing utensils*musculoskeletal pain; Low-stress mattress*musculoskeletal pain; Pain management*palliative care; Calcium and vitamin D*bone density; DEXA bone density scans*bone density; Routine eye exams*globus rupture; Retinal detachment; Glaucoma; Protective bandages*protection
-Treatment Efficacies: Ascorbic Acid (Vitamin C)*effective; Physical therapy*effective; Low-resistance exercise*effective; Calcium and vitamin D*effective; Routine eye exams*effective; Protective bandages*effective
-
- -
diff --git a/tests/output/eds-output.md b/tests/output/eds-output.md deleted file mode 100644 index dcd6c6d0b..000000000 --- a/tests/output/eds-output.md +++ /dev/null @@ -1,76 +0,0 @@ -# /Users/cjm/repos/ontogpt/tests/input/cases/treatment-eds.txt - -## Input - -_Disease: Ehlers Danlos Syndrome_ - -_Treatment:_ - -_The care of patients with EDS is generally focused on implementing preventative measures against serious or life-threatening complications. The primary complications seen in EDS involve the skin, musculoskeletal, and cardiovascular systems. Patient skin is velvety thin, loose, and stretchable. This predisposes patients to difficulties with wound healing. For both accidental and surgical wounds, deep stiches are applied generously. Superficial stiches are placed to carefully realign the skin to prevent scarring. Stiches are also left in for extended periods of time to allow best strengthening of the forming scar tissue. Ascorbic acid (Vitamin C) may be recommended to help reduce the easy bruising that accompanies EDS. Hypermobile joints easily dislocate. With each dislocation, subsequent dislocations are increasingly likely, therefore prevention is particularly important for quality of life. Heavy sports, lifting, and other strenuous efforts should be avoided due to the risk of inciting trauma. Blood vessel fragility increases the risk for serious bleeds and dissections. High blood pressure (hypertension) puts additional strain on the fragile vasculature and increases the risk for complications. Regular screening for hypertension and arterial disease should be conducted and treatment should be initiated early on. The best approaches to screening are by non-invasive technology: ultrasound, MRI, or CT. Arteriography, colonoscopy, and other similarly invasive screening procedures should be considered carefully for benefit versus risk. Surgery for non-life threatening conditions should also be carefully considered. Pregnancies should be followed by obstetricians that are well trained in dealing with high-risk pregnancies. Delivery can progress very quickly in EDS patients and it is yet unclear if there is an advantage to mothers to deliver by vaginal or cesarean routes. Expectant mothers with known aortic root dilations should have echocardiograms each trimester to observe for possible exacerbation. All EDS-affected individuals should seek immediate medical attention for any sudden or unexplained pains and consider wearing a MedicAlert bracelet to communicate their status as a patient with EDS should they lose consciousness._ - -__ - -_hEDS patients may especially benefit from physical therapy, low-resistance exercise, and assistive devices like braces, wheelchairs, and scooters. Comfortable writing utensils and a low-stress mattress serve an important role in reducing musculoskeletal pain. Pain management is tailored to the individual. Gastrointestinal and psychological complications are likewise managed per an individual’s needs. In addition to physical therapy and low-resistance exercise, calcium and vitamin D can help maximize bone density. DEXA bone density scans should be conducted every other year. kEDS patients should have routine eye exams as they are at risk for globus rupture, retinal detachment and glaucoma. dEDS patients may benefit from protective bandages over exposed areas such as the skin of the elbows and knees._ - -__ - -## Results - - - -### disease - - -- Ehlers Danlos Syndrome [MONDO:0020066](https://bioregistry.io/MONDO:0020066) - - -### drugs - - -- AUTO:Ascorbic%20Acid%20%28Vitamin%20C%29 - - -### treatments - - -- AUTO:Preventative%20measures - -- AUTO:Deep%20stiches - -- AUTO:Superficial%20stiches - -- AUTO:Ascorbic%20Acid%20%28Vitamin%20C%29 - -- AUTO:Avoidance%20of%20heavy%20sports%2C%20lifting%2C%20and%20other%20strenuous%20efforts - -- AUTO:Screening%20for%20hypertension%20and%20arterial%20disease - -- AUTO:Non-invasive%20technology%20screening - -- AUTO:Careful%20consideration%20of%20surgery%20for%20non-life%20threatening%20conditions - -- AUTO:Monitoring%20during%20pregnancy - -- Physical therapy [MAXO:0000011](https://bioregistry.io/MAXO:0000011) - -- AUTO:Low-resistance%20exercise - -- Assistive devices [NCIT:C157792](https://bioregistry.io/NCIT:C157792) - -- AUTO:Comfortable%20writing%20utensils - -- AUTO:Low-stress%20mattress - -- Pain management [MAXO:0000457](https://bioregistry.io/MAXO:0000457) - -- AUTO:Calcium%20and%20vitamin%20D - -- AUTO:DEXA%20bone%20density%20scans - -- AUTO:Routine%20eye%20exams - -- AUTO:Protective%20bandages - - -### contraindications - diff --git a/tests/output/gene_requests_cache.db b/tests/output/gene_requests_cache.db deleted file mode 100644 index 751bbb2ee..000000000 Binary files a/tests/output/gene_requests_cache.db and /dev/null differ diff --git a/tests/output/generalized-drug-mechanisms-001.yaml b/tests/output/generalized-drug-mechanisms-001.yaml deleted file mode 100644 index 14d01d8e4..000000000 --- a/tests/output/generalized-drug-mechanisms-001.yaml +++ /dev/null @@ -1,109 +0,0 @@ -- _combo: - - disease - - drug - _input: - disease: MESH:D014552 - drug: drugbank:DB00438 - input_id: null - input_text: 'example: - - disease: Leukemia, Myelogenous, Chronic, BCR-ABL Positive - - drug: Imatinib - - mechanism_links: tyrosine-protein kinase ABL1 (human) - decreases activity of - - Imatinib Mesylate; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - causes - - tyrosine-protein kinase ABL1 (human) - - - disease: Mastocytosis, Systemic - - drug: Imatinib - - mechanism_links: mast/stem cell growth factor receptor Kit (human) - decreases - activity of - Imatinib Mesylate; platelet-derived growth factor receptor alpha - (human) - decreases activity of - Imatinib Mesylate; cell population proliferation - - positively regulates - mast/stem cell growth factor receptor Kit (human); cell - population proliferation - positively regulates - platelet-derived growth factor - receptor alpha (human); Mastocytosis, Systemic - causes - cell population proliferation - - - disease: Pain - - drug: Acetaminophen - - mechanism_links: prostaglandin G/H synthase 1 (human) - decreases activity of - - Acetaminophen; prostaglandin G/H synthase 2 (human) - decreases activity of - - Acetaminophen; prostaglandin E synthase 3 (human) - decreases activity of - - Acetaminophen; prostaglandin biosynthetic process - positively regulates - prostaglandin - G/H synthase 1 (human); prostaglandin biosynthetic process - positively regulates - - prostaglandin G/H synthase 2 (human); prostaglandin biosynthetic process - positively - regulates - prostaglandin E synthase 3 (human); Prostaglandins - increases abundance - of - prostaglandin biosynthetic process; Pain - positively correlated with - Prostaglandins - - - disease: Fever - - drug: Acetaminophen - - mechanism_links: REACT:R-HSA-2162123 - negatively regulates - Acetaminophen; brain - - occurs in - REACT:R-HSA-2162123; temperature homeostasis - location of - brain; - Fever - negatively correlated with - temperature homeostasis - - - - - === - - - disease: Urinary Tract Infections - - drug: Ceftazidime - - ' - input_title: null - named_entities: - - id: MESH:D014552 - label: Urinary Tract Infections - - id: GO:0009273 - label: cell wall biosynthetic process - - id: RO:0002213 - label: positively regulates - - id: GO:0009273 - label: cell envelope biosynthetic process - - id: RO:0002213 - label: positively regulates - - id: MESH:D002442 - label: Ceftazidime - - id: RO:0001019 - label: contains - prompt: 'From the text below, extract the following entities in the following format: - - - subject: - - predicate: - - object: - - ' - raw_completion_output: null - results: - - disease: MESH:D014552 - drug: drugbank:DB00438 - mechanism_links: - - object: MESH:D014552 - predicate: biological process involved in - subject: Gram-negative bacilli - - object: Gram-negative bacilli - predicate: RO:0002213 - subject: GO:0009273 - - object: Gram-negative bacilli - predicate: RO:0002213 - subject: GO:0009273 - - object: MESH:D002442 - predicate: binds to - subject: penicillin binding proteins - - object: penicillin binding proteins - predicate: RO:0001019 - subject: Gram-negative bacilli diff --git a/tests/output/generalized-reactions-001.yaml b/tests/output/generalized-reactions-001.yaml deleted file mode 100644 index 0a0e8aa98..000000000 --- a/tests/output/generalized-reactions-001.yaml +++ /dev/null @@ -1,708 +0,0 @@ -- _combo: - - label - _input: - label: pseudouridine 5'-phosphatase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: pseudouridine 5''-phosphatase activity - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - id: null - label: pseudouridine 5'-phosphatase activity - left_side: - - CHEBI:18116 - - CHEBI:15377 - right_side: - - CHEBI:17802 - - CHEBI:26020 - subclass_of: nucleoside 5'-phosphatase activity - synonyms: [] -- _combo: - - description - _input: - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - description: Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - id: null - label: null - left_side: - - CHEBI:18116 - - CHEBI:15377 - right_side: - - CHEBI:17802 - - CHEBI:26020 - subclass_of: pseudouridine 5'-phosphate phosphohydrolase activity - synonyms: [] -- _combo: - - label - - description - _input: - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - label: pseudouridine 5'-phosphatase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: pseudouridine 5''-phosphatase activity - - description: Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: pseudouridine 5''-phosphate + H2O = pseudouridine - + phosphate.' - id: null - label: pseudouridine 5'-phosphatase activity - left_side: - - CHEBI:18116 - - CHEBI:15377 - right_side: - - CHEBI:17802 - - CHEBI:26020 - subclass_of: GO:0016791 - synonyms: [] -- _combo: - - label - _input: - label: L-altrarate dehydratase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: L-altrarate dehydratase activity - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: L-altrarate + H2O = 2-dehydro-3-deoxy-L-altronate - + H2.' - id: null - label: L-altrarate dehydratase activity - left_side: - - CHEBI:37547 - - CHEBI:15377 - right_side: - - 2-dehydro-3-deoxy-L-altronate - - CHEBI:18276 - subclass_of: amino acid dehydratase activity - synonyms: [] -- _combo: - - description - _input: - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - description: Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - - id: GO:0016491 - label: oxidoreductase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - id: null - label: null - left_side: - - CHEBI:37547 - right_side: - - CHEBI:16369 - - CHEBI:15377 - subclass_of: GO:0016491 - synonyms: [] -- _combo: - - label - - description - _input: - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - label: L-altrarate dehydratase activity - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - label: L-altrarate dehydratase activity - - description: Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O. - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - - id: GO:0016491 - label: oxidoreductase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - - id: GO:0016829 - label: lyase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - prompt: null - raw_completion_output: null - results: - - description: 'Catalysis of the reaction: L-altrarate = 5-dehydro-4-deoxy-D-glucarate - + H2O.' - id: null - label: L-altrarate dehydratase activity - left_side: - - CHEBI:37547 - right_side: - - CHEBI:16369 - - CHEBI:15377 - subclass_of: GO:0016829 - synonyms: [] -- _combo: - - description - _input: - description: ent-copalyl diphosphate + H2O = diphosphate + ent-manool - input_id: null - input_text: 'example: - - label: trans-hexaprenyltranstransferase activity - - description: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl - diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate. - - subclass_of: prenyltransferase activity - - left_side: (2E,6E)-farnesyl diphosphate; 4 isopentenyl diphosphate - - right_side: 4 diphosphate; all-trans-heptaprenyl diphosphate - - - label: dihydroorotate dehydrogenase (fumarate) activity - - description: Catalysis of the reaction: (S)-dihydroorotate + fumarate = orotate - + succinate. - - subclass_of: dihydroorotate dehydrogenase activity - - left_side: (S)-dihydroorotate; fumarate - - right_side: orotate; succinate - - - label: butanol dehydrogenase activity - - description: Catalysis of the reaction: butanal + NADH + H+ => n-butanol + NAD+. - - subclass_of: alcohol dehydrogenase (NAD+) activity - - left_side: butanal; NADPH; H+ - - right_side: butanol; NAD+ - - - - - === - - - description: ent-copalyl diphosphate + H2O = diphosphate + ent-manool - - ' - input_title: null - named_entities: - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: GO:0016791 - label: phosphatase activity - - id: CHEBI:18116 - label: pseudouridine 5'-phosphate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:17802 - label: pseudouridine - - id: CHEBI:26020 - label: phosphate - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18276 - label: H2 - - id: GO:0016491 - label: oxidoreductase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - - id: GO:0016829 - label: lyase activity - - id: CHEBI:37547 - label: L-altrarate - - id: CHEBI:16369 - label: 5-dehydro-4-deoxy-D-glucarate - - id: CHEBI:15377 - label: H2O - - id: GO:0016787 - label: hydrolase activity - - id: CHEBI:15377 - label: H2O - - id: CHEBI:18361 - label: diphosphate - - id: CHEBI:76948 - label: ent-manool - prompt: null - raw_completion_output: null - results: - - description: ent-copalyl diphosphate + H2O = diphosphate + ent-manool - id: null - label: Ent-copalyl-diphosphate DD-hydrolase activity - left_side: - - ent-copalyl-diphosphate - - CHEBI:15377 - right_side: - - CHEBI:18361 - - CHEBI:76948 - subclass_of: GO:0016787 - synonyms: [] diff --git a/tests/output/go-nucleus.hallucinated.halo.yaml b/tests/output/go-nucleus.hallucinated.halo.yaml deleted file mode 100644 index f36cf9d4f..000000000 --- a/tests/output/go-nucleus.hallucinated.halo.yaml +++ /dev/null @@ -1,408 +0,0 @@ -elements: -- name: Cell - context: subcellular - description: A material entity of anatomical origin (part of or deriving from an - organism) that has as its parts a maximally connected cell compartment surrounded - by a plasma membrane. - subclass_of: - - ConnectedAnatomicalStructure - parts: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Envelope -- name: Occurrent - context: subcellular - description: An entity that has temporal parts and that happens, unfolds or develops - through time. - subtypes: - - Process -- name: Membrane-boundedOrganelle - context: subcellular - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, - plastids, vacuoles, and vesicles. Excludes the plasma membrane. - synonyms: - - membrane-enclosed organelle - subclass_of: - - Organelle - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleMembrane - - OrganelleEnvelope - equivalent_to: Organelle and has part some Membrane -- name: MetabolicProcess - context: subcellular - description: The chemical reactions and pathways, including anabolism and catabolism, - by which living organisms transform chemical substances. Metabolic processes typically - transform small molecules, but also include macromolecular processes such as DNA - repair and replication, and protein synthesis and degradation. - synonyms: - - metabolism - - metabolic process resulting in cell growth - - metabolism resulting in cell growth - - multicellular organism metabolic process - - single-organism metabolic process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: NuclearMembrane - context: subcellular - description: Either of the lipid bilayers that surround the nucleus and form the - nuclear envelope; excludes the intermembrane space. - subclass_of: - - OrganelleMembrane - part_of: - - Nucleus - - NuclearEnvelope - equivalent_to: Membrane and part of some Nucleus -- name: Process - context: subcellular - description: An occurrent that has temporal proper parts and for some time t, p - s-depends_on some material entity at t. - subclass_of: - - Occurrent - subtypes: - - BiologicalProcess -- name: CellularComponent - context: subcellular - description: 'A location, relative to cellular compartments and structures, occupied - by a macromolecular machine when it carries out a molecular function. There are - two ways in which the gene ontology describes locations of gene products: (1) - relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or - compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes - of which they are parts (e.g., the ribosome).' - synonyms: - - cell or subcellular entity - - cellular component - - subcellular entity - subclass_of: - - MaterialEntity - subtypes: - - CellularAnatomicalEntity -- name: PhosphorusMetabolicProcess - context: subcellular - description: The chemical reactions and pathways involving the nonmetallic element - phosphorus or compounds that contain phosphorus, usually in the form of a phosphate - group (PO4). - synonyms: - - phosphorus metabolism - subclass_of: - - CellularMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some PhosphorusMolecularEntity -- name: BiologicalEntity - context: subcellular - subclass_of: - - IndependentContinuant - subtypes: - - AnatomicalEntity -- name: IntracellularMembrane-boundedOrganelle - context: subcellular - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane and occurring within the cell. Includes - the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma - membrane. - synonyms: - - intracellular membrane-enclosed organelle - subclass_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - Nucleus - equivalent_to: Membrane-boundedOrganelle and part of some IntracellularAnatomicalStructure -- name: Membrane - context: subcellular - description: A lipid bilayer along with all the proteins and protein complexes embedded - in it an attached to it. - synonyms: - - membrane region - - region of membrane - - whole membrane - subclass_of: - - CellularAnatomicalEntity - subtypes: - - OrganelleMembrane -- name: BiologicalProcess - context: subcellular - description: A biological process represents a specific objective that the organism - is genetically programmed to achieve. Biological processes are often described - by their outcome or ending state, e.g., the biological process of cell division - results in the creation of two daughter cells (a divided cell) from a single parent - cell. A biological process is accomplished by a particular set of molecular functions - carried out by specific gene products (or macromolecular complexes), often in - a highly regulated manner and in a particular temporal sequence. - synonyms: - - biological process - - physiological process - - single organism process - - single-organism process - subclass_of: - - Process - subtypes: - - MetabolicProcess - - CellularProcess -- name: MaterialAnatomicalEntity - context: subcellular - subclass_of: - - MaterialEntity - - AnatomicalEntity - subtypes: - - ConnectedAnatomicalStructure -- name: IntracellularAnatomicalStructure - context: subcellular - description: A component of a cell contained within (but not including) the plasma - membrane. In eukaryotes it includes the nucleus and cytoplasm. - synonyms: - - internal to cell - - intracellular - - protoplasm - - nucleocytoplasm - - protoplast - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - IntracellularOrganelle - - IntracellularMembrane-boundedOrganelle -- name: CellularMetabolicProcess - context: subcellular - description: The chemical reactions and pathways by which individual cells transform - chemical substances. - synonyms: - - cellular metabolism - - intermediary metabolism - subclass_of: - - MetabolicProcess - - CellularProcess - subtypes: - - PhosphorusMetabolicProcess -- name: Organelle - context: subcellular - description: Organized structure of distinctive morphology and function. Includes - the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, - and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes - the plasma membrane. - subclass_of: - - CellularAnatomicalEntity - subtypes: - - Membrane-boundedOrganelle - - IntracellularOrganelle -- name: Envelope - context: subcellular - description: A multilayered structure surrounding all or part of a cell; encompasses - one or more lipid bilayers, and may include a cell wall layer; also includes the - space between layers. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - subtypes: - - OrganelleEnvelope -- name: EndomembraneSystem - context: subcellular - description: A collection of membranous structures involved in transport within - the cell. The main components of the endomembrane system are endoplasmic reticulum, - Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane - system pass materials through each other or though the use of vesicles. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - NuclearEnvelope -- name: Nucleus - context: subcellular - description: A membrane-bounded organelle of eukaryotic cells in which chromosomes - are housed and replicated. In most cells, the nucleus contains all of the cell's - chromosomes except the organellar chromosomes, and is the site of RNA synthesis - and processing. In some species, or in specialized cell types, RNA metabolism - or DNA replication may be absent. - synonyms: - - cell nucleus - - horsetail nucleus - subclass_of: - - IntracellularMembrane-boundedOrganelle - parts: - - NuclearEnvelope - - NuclearMembrane -- name: MaterialEntity - context: subcellular - description: An independent continuant that is spatially extended whose identity - is independent of that of other entities and can be maintained through time. - subclass_of: - - IndependentContinuant - subtypes: - - MaterialAnatomicalEntity - - CellularComponent -- name: OrganelleMembrane - context: subcellular - description: A membrane that is one of the two lipid bilayers of an organelle envelope - or the outermost membrane of single membrane bound organelle. - synonyms: - - intracellular membrane - subclass_of: - - Membrane - part_of: - - Membrane-boundedOrganelle - subtypes: - - NuclearMembrane - equivalent_to: Membrane and part of some Membrane-boundedOrganelle -- name: IntracellularOrganelle - context: subcellular - description: Organized structure of distinctive morphology and function, occurring - within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, - ribosomes and the cytoskeleton. Excludes the plasma membrane. - subclass_of: - - Organelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleEnvelope - equivalent_to: Organelle and part of some IntracellularAnatomicalStructure -- name: NuclearEnvelope - context: subcellular - description: The double lipid bilayer enclosing the nucleus and separating its contents - from the rest of the cytoplasm; includes the intermembrane space, a gap of width - 20-40 nm (also called the perinuclear space). - subclass_of: - - OrganelleEnvelope - part_of: - - Nucleus - - EndomembraneSystem - parts: - - NuclearMembrane -- name: OrganelleEnvelope - context: subcellular - description: A double membrane structure enclosing an organelle, including two lipid - bilayers and the region between them. In some cases, an organelle envelope may - have more than two membranes. - subclass_of: - - Envelope - part_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - subtypes: - - NuclearEnvelope -- name: AnatomicalEntity - context: subcellular - subclass_of: - - BiologicalEntity - subtypes: - - MaterialAnatomicalEntity - - CellularAnatomicalEntity -- name: CellularAnatomicalEntity - context: subcellular - description: A part of a cellular organism that is either an immaterial entity or - a material entity with granularity above the level of a protein complex but below - that of an anatomical system. Or, a substance produced by a cellular organism - with granularity above the level of a protein complex. - subclass_of: - - AnatomicalEntity - - CellularComponent - subtypes: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Membrane - - Envelope - - Organelle -- name: Continuant - context: subcellular - description: An entity that exists in full at any time in which it exists at all, - persists through time while maintaining its identity and has no temporal parts. - subtypes: - - IndependentContinuant -- name: IndependentContinuant - context: subcellular - description: A continuant that is a bearer of quality and realizable entity entities, - in which other entities inhere and which itself cannot inhere in anything. - subclass_of: - - Continuant - subtypes: - - MaterialEntity - - BiologicalEntity -- name: CellularProcess - context: subcellular - description: Any process that is carried out at the cellular level, but not necessarily - restricted to a single cell. For example, cell communication occurs among more - than one cell, but occurs at the cellular level. - synonyms: - - cell physiology - - cellular physiological process - - cell growth and/or maintenance - - single-organism cellular process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: ConnectedAnatomicalStructure - context: subcellular - subclass_of: - - MaterialAnatomicalEntity - subtypes: - - Cell -- name: Axon - context: subcellular - description: The long process of a neuron that conducts nerve impulses, usually - away from the cell body to the terminals and varicosities, which are sites of - storage and release of neurotransmitter. - synonyms: - - process of Anaxonic cell - - process of neuron cell - subclass_of: - - PartOfSensorimotorSystem - - AnaxonicCellProcess - - Neuron - equivalent_to: Neuron and has part some '(process of Anaxonic cell) or (process - of neuron cell)' -- name: Dendrite - context: subcellular - description: a neuron's branched extension that conducts the reflex impulses to - the cell body - synonyms: - - ecdysone receptor - subclass_of: - - Axon - subtypes: - - Autograph - - Encephalograph - - Telegraph - - Timeograph - - Xylograph -- name: PartOfSensorimotorSystem - context: subcellular - subclass_of: - - NeurologicalTissue - - MobileAnatomicalStructure - part_of: - - WholeSensorimotorSystem - subtypes: - - AfferentNerve - - EfferentNerve - - Ganglion - - MotorSystem - - SensoryReceptor - - SomaticCentralNervousSystemCell - equivalent_to: NeuralTissue and part of some MobileAnatomicalStructure -- name: AnaxonicCellProcess - context: subcellular - part_of: - - CellProcess - - AnatomicalStructureProcess - - BiologicalProcess -- name: Neuron - context: subcellular - subtypes: - - CentralNervousSystemNeuron - - DorsalRootGangliaNeuron -- name: Segment - context: subcellular - description: Describes how we visually represent the context, that is what is written. - subtypes: - - Autinem, Automeme, Autoradic, Autoflume - equivalent_to: isWriteContextOf diff --git a/tests/output/go-nucleus.halo.yaml b/tests/output/go-nucleus.halo.yaml deleted file mode 100644 index 20386acda..000000000 --- a/tests/output/go-nucleus.halo.yaml +++ /dev/null @@ -1,318 +0,0 @@ -elements: -- name: PhosphorusMetabolicProcess - description: The chemical reactions and pathways involving the nonmetallic element - phosphorus or compounds that contain phosphorus, usually in the form of a phosphate - group (PO4). - synonyms: - - phosphorus metabolism - subclass_of: - - CellularMetabolicProcess - equivalent_to: MetabolicProcess and has primary input or output some PhosphorusMolecularEntity -- name: OrganelleMembrane - description: A membrane that is one of the two lipid bilayers of an organelle envelope - or the outermost membrane of single membrane bound organelle. - synonyms: - - intracellular membrane - subclass_of: - - Membrane - part_of: - - Membrane-boundedOrganelle - subtypes: - - NuclearMembrane - equivalent_to: Membrane and part of some Membrane-boundedOrganelle -- name: AnatomicalEntity - subclass_of: - - BiologicalEntity - subtypes: - - MaterialAnatomicalEntity - - CellularAnatomicalEntity -- name: NuclearMembrane - description: Either of the lipid bilayers that surround the nucleus and form the - nuclear envelope; excludes the intermembrane space. - subclass_of: - - OrganelleMembrane - part_of: - - Nucleus - - NuclearEnvelope - equivalent_to: Membrane and part of some Nucleus -- name: CellularAnatomicalEntity - description: A part of a cellular organism that is either an immaterial entity or - a material entity with granularity above the level of a protein complex but below - that of an anatomical system. Or, a substance produced by a cellular organism - with granularity above the level of a protein complex. - subclass_of: - - AnatomicalEntity - - CellularComponent - subtypes: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Membrane - - Envelope - - Organelle -- name: Cell - description: A material entity of anatomical origin (part of or deriving from an - organism) that has as its parts a maximally connected cell compartment surrounded - by a plasma membrane. - subclass_of: - - ConnectedAnatomicalStructure - parts: - - IntracellularAnatomicalStructure - - EndomembraneSystem - - Envelope -- name: CellularComponent - description: 'A location, relative to cellular compartments and structures, occupied - by a macromolecular machine when it carries out a molecular function. There are - two ways in which the gene ontology describes locations of gene products: (1) - relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or - compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes - of which they are parts (e.g., the ribosome).' - synonyms: - - cell or subcellular entity - - cellular component - - subcellular entity - subclass_of: - - MaterialEntity - subtypes: - - CellularAnatomicalEntity -- name: EndomembraneSystem - description: A collection of membranous structures involved in transport within - the cell. The main components of the endomembrane system are endoplasmic reticulum, - Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane - system pass materials through each other or though the use of vesicles. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - NuclearEnvelope -- name: IndependentContinuant - description: A continuant that is a bearer of quality and realizable entity entities, - in which other entities inhere and which itself cannot inhere in anything. - subclass_of: - - Continuant - subtypes: - - MaterialEntity - - BiologicalEntity -- name: IntracellularOrganelle - description: Organized structure of distinctive morphology and function, occurring - within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, - ribosomes and the cytoskeleton. Excludes the plasma membrane. - subclass_of: - - Organelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleEnvelope - equivalent_to: Organelle and part of some IntracellularAnatomicalStructure -- name: Process - description: An occurrent that has temporal proper parts and for some time t, p - s-depends_on some material entity at t. - subclass_of: - - Occurrent - subtypes: - - BiologicalProcess -- name: OrganelleEnvelope - description: A double membrane structure enclosing an organelle, including two lipid - bilayers and the region between them. In some cases, an organelle envelope may - have more than two membranes. - subclass_of: - - Envelope - part_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - subtypes: - - NuclearEnvelope -- name: IntracellularAnatomicalStructure - description: A component of a cell contained within (but not including) the plasma - membrane. In eukaryotes it includes the nucleus and cytoplasm. - synonyms: - - internal to cell - - intracellular - - protoplasm - - nucleocytoplasm - - protoplast - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - parts: - - IntracellularOrganelle - - IntracellularMembrane-boundedOrganelle -- name: Organelle - description: Organized structure of distinctive morphology and function. Includes - the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, - and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes - the plasma membrane. - subclass_of: - - CellularAnatomicalEntity - subtypes: - - Membrane-boundedOrganelle - - IntracellularOrganelle -- name: MaterialAnatomicalEntity - subclass_of: - - MaterialEntity - - AnatomicalEntity - subtypes: - - ConnectedAnatomicalStructure -- name: ConnectedAnatomicalStructure - subclass_of: - - MaterialAnatomicalEntity - subtypes: - - Cell -- name: Membrane-boundedOrganelle - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, - plastids, vacuoles, and vesicles. Excludes the plasma membrane. - synonyms: - - membrane-enclosed organelle - subclass_of: - - Organelle - subtypes: - - IntracellularMembrane-boundedOrganelle - parts: - - OrganelleMembrane - - OrganelleEnvelope - equivalent_to: Organelle and has part some Membrane -- name: Membrane - description: A lipid bilayer along with all the proteins and protein complexes embedded - in it an attached to it. - synonyms: - - membrane region - - region of membrane - - whole membrane - subclass_of: - - CellularAnatomicalEntity - subtypes: - - OrganelleMembrane -- name: Continuant - description: An entity that exists in full at any time in which it exists at all, - persists through time while maintaining its identity and has no temporal parts. - subtypes: - - IndependentContinuant -- name: Nucleus - description: A membrane-bounded organelle of eukaryotic cells in which chromosomes - are housed and replicated. In most cells, the nucleus contains all of the cell's - chromosomes except the organellar chromosomes, and is the site of RNA synthesis - and processing. In some species, or in specialized cell types, RNA metabolism - or DNA replication may be absent. - synonyms: - - cell nucleus - - horsetail nucleus - subclass_of: - - IntracellularMembrane-boundedOrganelle - parts: - - NuclearEnvelope - - NuclearMembrane -- name: MetabolicProcess - description: The chemical reactions and pathways, including anabolism and catabolism, - by which living organisms transform chemical substances. Metabolic processes typically - transform small molecules, but also include macromolecular processes such as DNA - repair and replication, and protein synthesis and degradation. - synonyms: - - metabolism - - metabolic process resulting in cell growth - - metabolism resulting in cell growth - - multicellular organism metabolic process - - single-organism metabolic process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: BiologicalProcess - description: A biological process represents a specific objective that the organism - is genetically programmed to achieve. Biological processes are often described - by their outcome or ending state, e.g., the biological process of cell division - results in the creation of two daughter cells (a divided cell) from a single parent - cell. A biological process is accomplished by a particular set of molecular functions - carried out by specific gene products (or macromolecular complexes), often in - a highly regulated manner and in a particular temporal sequence. - synonyms: - - biological process - - physiological process - - single organism process - - single-organism process - subclass_of: - - Process - subtypes: - - MetabolicProcess - - CellularProcess -- name: Envelope - description: A multilayered structure surrounding all or part of a cell; encompasses - one or more lipid bilayers, and may include a cell wall layer; also includes the - space between layers. - subclass_of: - - CellularAnatomicalEntity - part_of: - - Cell - subtypes: - - OrganelleEnvelope -- name: CellularProcess - description: Any process that is carried out at the cellular level, but not necessarily - restricted to a single cell. For example, cell communication occurs among more - than one cell, but occurs at the cellular level. - synonyms: - - cell physiology - - cellular physiological process - - cell growth and/or maintenance - - single-organism cellular process - subclass_of: - - BiologicalProcess - subtypes: - - CellularMetabolicProcess -- name: CellularMetabolicProcess - description: The chemical reactions and pathways by which individual cells transform - chemical substances. - synonyms: - - cellular metabolism - - intermediary metabolism - subclass_of: - - MetabolicProcess - - CellularProcess - subtypes: - - PhosphorusMetabolicProcess -- name: Occurrent - description: An entity that has temporal parts and that happens, unfolds or develops - through time. - subtypes: - - Process -- name: MaterialEntity - description: An independent continuant that is spatially extended whose identity - is independent of that of other entities and can be maintained through time. - subclass_of: - - IndependentContinuant - subtypes: - - MaterialAnatomicalEntity - - CellularComponent -- name: BiologicalEntity - subclass_of: - - IndependentContinuant - subtypes: - - AnatomicalEntity -- name: NuclearEnvelope - description: The double lipid bilayer enclosing the nucleus and separating its contents - from the rest of the cytoplasm; includes the intermembrane space, a gap of width - 20-40 nm (also called the perinuclear space). - subclass_of: - - OrganelleEnvelope - part_of: - - Nucleus - - EndomembraneSystem - parts: - - NuclearMembrane -- name: IntracellularMembrane-boundedOrganelle - description: Organized structure of distinctive morphology and function, bounded - by a single or double lipid bilayer membrane and occurring within the cell. Includes - the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma - membrane. - synonyms: - - intracellular membrane-enclosed organelle - subclass_of: - - Membrane-boundedOrganelle - - IntracellularOrganelle - part_of: - - IntracellularAnatomicalStructure - subtypes: - - Nucleus - equivalent_to: Membrane-boundedOrganelle and part of some IntracellularAnatomicalStructure diff --git a/tests/output/gocam-27929086.pickle b/tests/output/gocam-27929086.pickle deleted file mode 100644 index 5834cd89e..000000000 Binary files a/tests/output/gocam-27929086.pickle and /dev/null differ diff --git a/tests/output/gocam-27929086.yaml b/tests/output/gocam-27929086.yaml deleted file mode 100644 index 48ce6b4cb..000000000 --- a/tests/output/gocam-27929086.yaml +++ /dev/null @@ -1,137 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/gocam-27929086.txt -input_text: "Title: The E3 ubiquitin ligase TRIM31 attenuates NLRP3 inflammasome\n\ - activation by promoting proteasomal degradation of NLRP3\n\nAbstract: The NLRP3\ - \ inflammasome has a fundamental role in host\ndefence against microbial pathogens\ - \ and its deregulation may cause\ndiverse inflammatory diseases. NLRP3 protein expression\ - \ is a\nrate-limiting step for inflammasome activation, thus its expression\nmust\ - \ be tightly controlled to maintain immune homeostasis and avoid\ndetrimental effects.\ - \ However, how NLRP3 expression is regulated\nremains largely unknown. In this study,\ - \ we identify E3 ubiquitin\nligase TRIM31 as a feedback suppressor of NLRP3 inflammasome.\ - \ TRIM31\ndirectly binds to NLRP3, promotes K48-linked polyubiquitination and\n\ - proteasomal degradation of NLRP3. Consequently, TRIM31 deficiency\nenhances NLRP3\ - \ inflammasome activation and aggravates alum-induced\nperitonitis in vivo. Furthermore,\ - \ TRIM31 deficiency attenuates the\nseverity of dextran sodium sulfate (DSS)-induced\ - \ colitis, an\ninflammatory bowel diseases model in which NLRP3 possesses protective\n\ - roles. Thus, our research describes a mechanism by which TRIM31 limits\nNLRP3 inflammasome\ - \ activity under physiological conditions and\nsuggests TRIM31 as a potential therapeutic\ - \ target for the intervention\nof NLRP3 inflammasome related diseases.\n\nFigure\ - \ 1: TRIM31 specifically inhibits NLRP3 inflammasome activation\nFigure 2. TRIM31\ - \ promotes proteasomal degradation of NLRP3\nFigure 3. TRIM31 interacts with NLRP3\n\ - Figure 4. TRIM31 promotes K48-linked polyubiquitination of NLRP3.\nFigure 5. IL-1\u03B2\ - \ and LPS induce TRIM31 expression\nFigure 6. TRIM31 deficiency enhances IL-1\u03B2\ - \ secretion and aggravates\nAlum-induced peritonitis in vivo\nFigure 7. TRIM31 deficiency\ - \ ameliorates DSS-induced colitis\nFigure 8. Working model for TRIM31 inhibiting\ - \ NLRP3 inflammasome activation.\n" -raw_completion_output: "\ngenes: TRIM31; NLRP3; IL-1\u03B2; LPS\norganisms: Homo sapiens;\ - \ Mus musculus\ngene_organisms: TRIM31*:Homo sapiens; NLRP3*:Homo sapiens; IL-1\u03B2\ - *:Homo sapiens; LPS*:Homo sapiens\nactivities: binding; K48-linked polyubiquitination;\ - \ proteasomal degradation; expression; secrection\ngene_functions: TRIM31*:binding;\ - \ TRIM31*:K48-linked polyubiquitination; TRIM31*:proteasomal degradation; NLRP3*:expression;\ - \ IL-1\u03B2*:secretion\ncellular_processes: inflammasome activation; immune homeostasis\n\ - pathways: NLRP3 inflammasome\ngene_gene_interactions: TRIM31*:NLRP3; IL-1\u03B2\ - *:LPS\ngene_localizations: TRIM31*/cytoplasm; NLRP3*/mitochondrion" -prompt: 'Split the following piece of text into fields in the following format: - - - gene: - - location: - - - - Text: - - NLRP3*/mitochondrion - - - === - - - ' -extracted_object: - genes: - - HGNC:16289 - - HGNC:16400 - - HGNC:5992 - - HGNC:6121 - organisms: - - NCBITaxon:9606 - - NCBITaxon:10090 - gene_organisms: - - gene: AUTO:TRIM31%2A - organism: NCBITaxon:9606 - - gene: AUTO:NLRP3%2A - organism: NCBITaxon:9606 - - gene: AUTO:IL-1%CE%B2%2A - organism: NCBITaxon:9606 - - gene: AUTO:LPS%2A - organism: NCBITaxon:9606 - activities: - - GO:0005488 - - AUTO:K48-linked%20polyubiquitination - - AUTO:proteasomal%20degradation - - AUTO:expression - - AUTO:secrection - gene_functions: - - gene: AUTO:TRIM31%2A - molecular_activity: GO:0005488 - - gene: AUTO:TRIM31%2A - molecular_activity: AUTO:K48-linked%20polyubiquitination - - gene: AUTO:TRIM31%2A - molecular_activity: AUTO:proteasomal%20degradation - - gene: AUTO:NLRP3%2A - molecular_activity: AUTO:Expression - - gene: AUTO:IL-1%CE%B2%2A - molecular_activity: GO:0046903 - cellular_processes: - - AUTO:inflammasome%20activation - - AUTO:immune%20homeostasis - pathways: - - AUTO:NLRP3%20inflammasome - gene_gene_interactions: - - gene1: AUTO:TRIM31%2A - gene2: HGNC:16400 - - gene1: AUTO:IL-1%CE%B2%2A - gene2: HGNC:6121 - gene_localizations: - - gene: AUTO:TRIM31%2A - location: GO:0005737 - - gene: HGNC:16400 - location: GO:0005739 -named_entities: -- id: HGNC:16289 - label: TRIM31 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:5992 - label: "IL-1\u03B2" -- id: HGNC:6121 - label: LPS -- id: MESH:D006801 - label: Homo sapiens -- id: NCBITaxon:10090 - label: Mus musculus -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0005488 - label: binding -- id: GO:0005488 - label: binding -- id: GO:0046903 - label: secretion -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:6121 - label: LPS -- id: GO:0005737 - label: cytoplasm -- id: HGNC:16400 - label: NLRP3 -- id: GO:0005739 - label: mitochondrion diff --git a/tests/output/gocam-33246504.pickle b/tests/output/gocam-33246504.pickle deleted file mode 100644 index c18082890..000000000 Binary files a/tests/output/gocam-33246504.pickle and /dev/null differ diff --git a/tests/output/gocam-33246504.yaml b/tests/output/gocam-33246504.yaml deleted file mode 100644 index f741fcc99..000000000 --- a/tests/output/gocam-33246504.yaml +++ /dev/null @@ -1,216 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/gocam-33246504.txt -input_text: "Text: An allosteric interleukin-1 receptor modulator mitigates\ninflammation\ - \ and photoreceptor toxicity in a model of retinal\ndegeneration\n\nBackground:\ - \ Inflammation and particularly interleukin-1\u03B2 (IL-1\u03B2), a pro-inflammatory\ - \ cytokine highly secreted by activated immune cells during early AMD pathological\ - \ events, contribute significantly to retinal neurodegeneration. Here, we identify\ - \ specific cell types that generate IL-1\u03B2 and harbor the IL-1 receptor (IL-1R)\ - \ and pharmacologically validate IL-1\u03B2's contribution to neuro-retinal degeneration\ - \ using the IL-1R allosteric modulator composed of the amino acid sequence rytvela\ - \ (as well as the orthosteric antagonist, Kineret) in a model of blue light-induced\ - \ retinal degeneration.\n\nMethods: Mice were exposed to blue light for 6 h and\ - \ sacrificed 3 days later. Mice were intraperitoneally injected with rytvela, Kineret,\ - \ or vehicle twice daily for 3 days. The inflammatory markers F4/80, NLRP3, caspase-1,\ - \ and IL-1\u03B2 were assessed in the retinas. Single-cell RNA sequencing was used\ - \ to determine the cell-specific expression patterns of retinal Il1b and Il1r1.\ - \ Macrophage-induced photoreceptor death was assessed ex vivo using retinal explants\ - \ co-cultured with LPS-activated bone marrow-derived macrophages. Photoreceptor\ - \ cell death was evaluated by the TUNEL assay. Retinal function was assessed by\ - \ flash electroretinography.\n\nResults: Blue light markedly increased the mononuclear\ - \ phagocyte recruitment and levels of inflammatory markers associated with photoreceptor\ - \ death. Co-localization of NLRP3, caspase-1, and IL-1\u03B2 with F4/80+ mononuclear\ - \ phagocytes was clearly detected in the subretinal space, suggesting that these\ - \ inflammatory cells are the main source of IL-1\u03B2. Single-cell RNA sequencing\ - \ confirmed the immune-specific expression of Il1b and notably perivascular macrophages\ - \ in light-challenged mice, while Il1r1 expression was found primarily in astrocytes,\ - \ bipolar, and vascular cells. Retinal explants co-cultured with LPS/ATP-activated\ - \ bone marrow-derived macrophages displayed a high number of TUNEL-positive photoreceptors,\ - \ which was abrogated by rytvela treatment. IL-1R antagonism significantly mitigated\ - \ the inflammatory response triggered in vivo by blue light exposure, and rytvela\ - \ was superior to Kineret in preserving photoreceptor density and retinal function.\n\ - \nConclusion: These findings substantiate the importance of IL-1\u03B2 in neuro-retinal\ - \ degeneration and revealed specific sources of Il1b from perivascular MPs, with\ - \ its receptor Ilr1 being separately expressed on surrounding neuro-vascular and\ - \ astroglial cells. They also validate the efficacy of rytvela-induced IL-1R modulation\ - \ in suppressing detrimental inflammatory responses and preserving photoreceptor\ - \ density and function in these conditions, reinforcing the rationale for clinical\ - \ translation.\n\nKeywords: Inflammasome; Inflammation; Interleukin-1; Interleukin-1\ - \ receptor; Photoreceptors; Retinal degeneration; Rytvela; cell death.\n" -raw_completion_output: "\ngenes: Il1b; Il1r1; NLRP3; caspase-1; F4/80;\norganisms:\ - \ Mus Musculus;\ngene_organisms: Il1b / Mus Musculus; Il1r1 / Mus Musculus; NLRP3\ - \ / Mus Musculus; caspase-1 / Mus Musculus; F4/80 / Mus Musculus; \nactivities:\ - \ targeting; suppressing; validating;\ngene_functions: Il1b / targeting; Il1r1 /\ - \ targeting; NLRP3 / targeting; caspase-1 / targeting; F4/80 / targeting; rytvela\ - \ / suppressing; Kineret / suppressing;\ncellular_processes: neuro-retinal degeneration;\ - \ neuronal ativation; macrophage-induced photoreceptor death;\npathways: interleukin-1\ - \ pathway;\ngene_gene_interactions: Il1b and Il1r1; NLRP3 and caspase-1;\ngene_localizations:\ - \ Il1b / perivascular macrophages; Il1r1 / astrocytes, bipolar, and vascular cells;\ - \ NLRP3 / subretinal space; caspase-1 / subretinal space; F4/80 / mononuclear phagocytes." -prompt: 'Split the following piece of text into fields in the following format: - - - gene: - - location: - - - - Text: - - F4/80 / mononuclear phagocytes. - - - === - - - ' -extracted_object: - genes: - - HGNC:5992 - - HGNC:5993 - - HGNC:16400 - - HGNC:1499 - - AUTO:F4/80 - organisms: - - NCBITaxon:10090 - gene_organisms: - - gene: HGNC:5992 - organism: NCBITaxon:10090 - - gene: HGNC:5993 - organism: NCBITaxon:10090 - - gene: HGNC:16400 - organism: NCBITaxon:10090 - - gene: HGNC:1499 - organism: NCBITaxon:10090 - - gene: AUTO:F4/80 - organism: NCBITaxon:10090 - activities: - - AUTO:targeting - - AUTO:suppressing - - AUTO:validating - gene_functions: - - gene: HGNC:5992 - molecular_activity: AUTO:targeting - - gene: HGNC:5993 - molecular_activity: AUTO:targeting - - gene: HGNC:16400 - molecular_activity: AUTO:targeting - - gene: HGNC:1499 - molecular_activity: AUTO:targeting - - gene: AUTO:F4/80 - molecular_activity: AUTO:Targeting - - gene: AUTO:rytvela - molecular_activity: AUTO:suppressing - - gene: AUTO:Kineret - molecular_activity: AUTO:suppressing - cellular_processes: - - AUTO:neuro-retinal%20degeneration - - AUTO:neuronal%20ativation - - AUTO:macrophage-induced%20photoreceptor%20death - pathways: - - AUTO:interleukin-1%20pathway - gene_gene_interactions: - - gene1: HGNC:5992 - gene2: HGNC:5993 - - gene1: HGNC:16400 - gene2: HGNC:1499 - gene_localizations: - - gene: HGNC:5992 - location: AUTO:Perivascular%20Macrophages - - gene: HGNC:5993 - location: AUTO:astrocytes%2C%20bipolar%2C%20and%20vascular%20cells - - gene: HGNC:16400 - location: AUTO:subretinal%20space - - gene: HGNC:1499 - location: AUTO:subretinal%20space - - gene: AUTO:F4/80 - location: AUTO:mononuclear%20phagocytes -named_entities: -- id: HGNC:16289 - label: TRIM31 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:5992 - label: "IL-1\u03B2" -- id: HGNC:6121 - label: LPS -- id: MESH:D006801 - label: Homo sapiens -- id: NCBITaxon:10090 - label: Mus musculus -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0005488 - label: binding -- id: GO:0005488 - label: binding -- id: GO:0046903 - label: secretion -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:6121 - label: LPS -- id: GO:0005737 - label: cytoplasm -- id: HGNC:16400 - label: NLRP3 -- id: GO:0005739 - label: mitochondrion -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5993 - label: Il1r1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:16400 - label: NLRP3 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 diff --git a/tests/output/gocam-betacat.pickle b/tests/output/gocam-betacat.pickle deleted file mode 100644 index 1615c136c..000000000 Binary files a/tests/output/gocam-betacat.pickle and /dev/null differ diff --git a/tests/output/gocam-betacat.yaml b/tests/output/gocam-betacat.yaml deleted file mode 100644 index f93759905..000000000 --- a/tests/output/gocam-betacat.yaml +++ /dev/null @@ -1,279 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/gocam-betacat.txt -input_text: "Title: \u03B2-Catenin Is Required for the cGAS/STING Signaling Pathway\ - \ but Antagonized by the Herpes Simplex Virus 1 US3 Protein\nText:\nThe cGAS/STING-mediated\ - \ DNA-sensing signaling pathway is crucial\nfor interferon (IFN) production and\ - \ host antiviral\nresponses. Herpes simplex virus I (HSV-1) is a DNA virus that\ - \ has\nevolved multiple strategies to evade host immune responses. Here,\nwe demonstrate\ - \ that the highly conserved \u03B2-catenin protein in the\nWnt signaling pathway\ - \ is an important factor to enhance the\ntranscription of type I interferon (IFN-I)\ - \ in the cGAS/STING\nsignaling pathway, and the production of IFN-I mediated by\n\ - \u03B2-catenin was antagonized by HSV-1 US3 protein via its kinase\nactivity. Infection\ - \ by US3-deficienct HSV-1 and its kinase-dead\nvariants failed to downregulate IFN-I\ - \ and IFN-stimulated\ngene (ISG) production induced by \u03B2-catenin. Consistent\ - \ with this,\nabsence of \u03B2-catenin enhanced the replication of US3-deficienct\n\ - HSV-1, but not wild-type HSV-1. The underlying mechanism was the\ninteraction of\ - \ US3 with \u03B2-catenin and its hyperphosphorylation of\n\u03B2-catenin at Thr556\ - \ to block its nuclear translocation. For the\nfirst time, HSV-1 US3 has been shown\ - \ to inhibit IFN-I production\nthrough hyperphosphorylation of \u03B2-catenin and\ - \ to subvert host\nantiviral innate immunity.IMPORTANCE Although increasing evidence\n\ - has demonstrated that HSV-1 subverts host immune responses and\nestablishes lifelong\ - \ latent infection, the molecular mechanisms\nby which HSV-1 interrupts antiviral\ - \ innate immunity, especially\nthe cGAS/STING-mediated cellular DNA-sensing signaling\ - \ pathway,\nhave not been fully explored. Here, we show that \u03B2-catenin\npromotes\ - \ cGAS/STING-mediated activation of the IFN pathway, which\nis important for cellular\ - \ innate immune responses and intrinsic\nresistance to DNA virus infection. The\ - \ protein kinase US3\nantagonizes the production of IFN by targeting \u03B2-catenin\ - \ via its\nkinase activity. The findings in this study reveal a novel\nmechanism\ - \ for HSV-1 to evade host antiviral immunity and add new\nknowledge to help in understanding\ - \ the interaction between the\nhost and HSV-1 infection.\n\nKeywords: HSV-1; US3;\ - \ type I IFN; \u03B2-catenin." -raw_completion_output: "genes: cGAS; STING; \u03B2-catenin; US3; IFN; ISG; Thr556\n\ - organisms: Homo sapiens; Herpes simplex virus I\ngene_organisms: cGAS/Homo sapiens;\ - \ STING/Homo sapiens; \u03B2-catenin/Homo sapiens; US3/Herpes simplex virus I; IFN/Homo\ - \ sapiens; ISG/Homo sapiens; Thr556/Homo sapiens\nactivities: transcription; replication;\ - \ production; nuclear translocation\ngene_functions: cGAS/activate type I IFN; STING/activate\ - \ type I IFN; \u03B2-catenin/enhance transcription of type I IFN; US3/antagonize\ - \ production of IFN; IFN/produce type I IFN; ISG/produce type I IFN; Thr556/block\ - \ nuclear translocation\ncellular_processes: DNA-sensing; interferon production;\ - \ host antiviral responses; Wnt signaling; hyperphosphorylation\npathways: cGAS/STING\ - \ signaling; Wnt signaling\ngene_gene_interactions: US3/\u03B2-catenin\ngene_localizations:\ - \ cGAS/--; STING/--; \u03B2-catenin/nuclear; US3/--; IFN/--; ISG/--; Thr556/--" -prompt: 'Split the following piece of text into fields in the following format: - - - gene: - - location: - - - - Text: - - Thr556/-- - - - === - - - ' -extracted_object: - genes: - - HGNC:21367 - - HGNC:27962 - - HGNC:2514 - - AUTO:US3 - - HGNC:5417 - - AUTO:ISG - - AUTO:Thr556 - organisms: - - NCBITaxon:9606 - - NCBITaxon:10298 - gene_organisms: - - gene: HGNC:21367 - organism: NCBITaxon:9606 - - gene: HGNC:27962 - organism: NCBITaxon:9606 - - gene: HGNC:2514 - organism: NCBITaxon:9606 - - gene: AUTO:US3 - organism: NCBITaxon:10298 - - gene: HGNC:5417 - organism: NCBITaxon:9606 - - gene: AUTO:ISG - organism: NCBITaxon:9606 - - gene: AUTO:Thr556 - organism: NCBITaxon:9606 - activities: - - GO:0006351 - - AUTO:replication - - AUTO:production - - AUTO:nuclear%20translocation - gene_functions: - - gene: HGNC:21367 - molecular_activity: AUTO:activate%20type%20I%20IFN - - gene: HGNC:27962 - molecular_activity: AUTO:activate%20type%20I%20IFN - - gene: HGNC:2514 - molecular_activity: AUTO:enhance%20transcription%20of%20type%20I%20IFN - - gene: AUTO:US3 - molecular_activity: AUTO:antagonize%20production%20of%20IFN - - gene: HGNC:5417 - molecular_activity: AUTO:produce%20type%20I%20IFN - - gene: AUTO:ISG - molecular_activity: AUTO:produce%20type%20I%20IFN - - gene: AUTO:Thr556 - molecular_activity: AUTO:block%20nuclear%20translocation - cellular_processes: - - AUTO:DNA-sensing - - GO:0001816 - - AUTO:host%20antiviral%20responses - - AUTO:Wnt%20signaling - - GO:0048151 - pathways: - - AUTO:cGAS/STING%20signaling - - AUTO:Wnt%20signaling - gene_gene_interactions: - - gene1: AUTO:US3 - gene2: HGNC:2514 - gene_localizations: - - gene: HGNC:21367 - location: AUTO:-- - - gene: HGNC:27962 - location: AUTO:-- - - gene: HGNC:2514 - location: AUTO:nuclear - - gene: AUTO:US3 - location: AUTO:-- - - gene: HGNC:5417 - location: AUTO:-- - - gene: AUTO:ISG - location: AUTO:-- - - gene: AUTO:Thr556 - location: AUTO:-- -named_entities: -- id: HGNC:16289 - label: TRIM31 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:5992 - label: "IL-1\u03B2" -- id: HGNC:6121 - label: LPS -- id: MESH:D006801 - label: Homo sapiens -- id: NCBITaxon:10090 - label: Mus musculus -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0005488 - label: binding -- id: GO:0005488 - label: binding -- id: GO:0046903 - label: secretion -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:6121 - label: LPS -- id: GO:0005737 - label: cytoplasm -- id: HGNC:16400 - label: NLRP3 -- id: GO:0005739 - label: mitochondrion -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5993 - label: Il1r1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:16400 - label: NLRP3 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:1499 - label: caspase-1 -- id: NCBITaxon:10090 - label: Mus Musculus -- id: NCBITaxon:10090 - label: Mus Musculus -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:5992 - label: Il1b -- id: HGNC:5993 - label: Il1r1 -- id: HGNC:16400 - label: NLRP3 -- id: HGNC:1499 - label: caspase-1 -- id: HGNC:21367 - label: cGAS -- id: HGNC:27962 - label: STING -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:5417 - label: IFN -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D018259 - label: Herpes simplex virus I -- id: HGNC:21367 - label: cGAS -- id: MESH:D006801 - label: Homo sapiens -- id: HGNC:27962 - label: STING -- id: MESH:D006801 - label: Homo sapiens -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D018259 - label: Herpes simplex virus I -- id: HGNC:5417 - label: IFN -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: MESH:D006801 - label: Homo sapiens -- id: GO:0006351 - label: transcription -- id: HGNC:21367 - label: cGAS -- id: HGNC:27962 - label: STING -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:5417 - label: IFN -- id: GO:0001816 - label: interferon production -- id: GO:0048151 - label: hyperphosphorylation -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:21367 - label: cGAS -- id: HGNC:27962 - label: STING -- id: HGNC:2514 - label: "\u03B2-catenin" -- id: HGNC:5417 - label: IFN diff --git a/tests/output/mendelian-disease-cmt2e-summary.pickle b/tests/output/mendelian-disease-cmt2e-summary.pickle deleted file mode 100644 index 458f3be2e..000000000 Binary files a/tests/output/mendelian-disease-cmt2e-summary.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-cmt2e-summary.yaml b/tests/output/mendelian-disease-cmt2e-summary.yaml deleted file mode 100644 index 47dc67651..000000000 --- a/tests/output/mendelian-disease-cmt2e-summary.yaml +++ /dev/null @@ -1,63 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-cmt2e-summary.txt -input_text: "CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2E; CMT2E\n\nINHERITANCE\n\ - - Autosomal dominant\nHEAD & NECK\nFace\n- Facial muscle weakness (in some patients)\n\ - Eyes\n- Ptosis (in some patients) \nMouth\n- High-arched palate (in some patients)\n\ - SKELETAL\n- Joint contractures\nSpine\n- Scoliosis (in some patients)\nHands\n-\ - \ Claw hand deformities (in severe cases)\nFeet\n- Pes cavus \n- Hammer toes\n-\ - \ Foot deformities\nMUSCLE, SOFT TISSUES\n- Shoulder muscle weakness (in some patients)\n\ - - Hypotrophy of the small hand muscles\n- Fiber-type predominance seen on muscle\ - \ biopsy (in some patients)\n- Fiber size variation (in some patients)\n- Internal\ - \ nuclei (in some patients)\n- Increased connective tissue (in some patients)\n\ - - Nemaline rods (in some patients)\n- Group fiber atrophy (in some patients)\n-\ - \ Angular fibers (in some patients)\n- EMG consistent with chronic neurogenic disorder\n\ - NEUROLOGIC\nCentral Nervous System\n- Delayed motor development (in some patients)\n\ - Peripheral Nervous System\n- Distal limb muscle weakness due to peripheral neuropathy\n\ - - Distal limb muscle atrophy due to peripheral neuropathy\n- 'Steppage' gait\n-\ - \ Foot drop\n- Distal sensory impairment\n- Hyporeflexia\n- Areflexia\n- Normal\ - \ or mildly decreased motor nerve conduction velocity (NCV) (greater than 38 m/s)\n\ - - Axonopathy seen on nerve biopsy\n- Giant axons with accumulation of disorganized\ - \ neurofilaments\nMISCELLANEOUS\n- Variable age of onset (range first to third decade)\n\ - - Usually begins in feet and legs (peroneal distribution)\n- Upper limb involvement\ - \ occurs later\n- Variable severity\n- Some patients may become wheelchair-bound\n\ - MOLECULAR BASIS\n- Caused by mutation in the light polypeptide neurofilament protein\ - \ gene (NEFL, 162280.0001)\n" -raw_completion_output: "name: Charcot-Marie-Tooth Disease, Axonal, Type 2E \ndescription:\ - \ A peripheral neuropathy characterized by distal limb muscle weakness and atrophy,\ - \ 'steppage' gait, foot drop, distal sensory impairment, hyporeflexia, areflexia,\ - \ and normal or mildly decreased motor nerve conduction velocity \nsynonyms: CMT2E\n\ - subclass_of; Charcot-Marie-Tooth Disease\nsymptoms: Facial muscle weakness; Ptosis;\ - \ High-arched palate; Joint contractures; Scoliosis; Claw hand deformities; Pes\ - \ cavus; Hammer toes; Foot deformities; Shoulder muscle weakness; Hypotrophy of\ - \ the small hand muscles; Delayed motor development\ninheritance: Autosomal dominant\n\ - genes: NEFL\ndisease_onsets: Adult; Juvenile; First decade\nlabel: Charcot-Marie-Tooth\ - \ Disease, Axonal, Type 2E" -prompt: "From the text below, extract the following entities in the following format:\n\ - \nname: \ndescription: \n\ - synonyms: \nsubclass_of: \nsymptoms: \ninheritance:\ - \ \ngenes: \ndisease_onsets: \n\ - label: \n\n\nText:\nCHARCOT-MARIE-TOOTH DISEASE,\ - \ AXONAL, TYPE 2E; CMT2E\n\nINHERITANCE\n- Autosomal dominant\nHEAD & NECK\nFace\n\ - - Facial muscle weakness (in some patients)\nEyes\n- Ptosis (in some patients) \n\ - Mouth\n- High-arched palate (in some patients)\nSKELETAL\n- Joint contractures\n\ - Spine\n- Scoliosis (in some patients)\nHands\n- Claw hand deformities (in severe\ - \ cases)\nFeet\n- Pes cavus \n- Hammer toes\n- Foot deformities\nMUSCLE, SOFT TISSUES\n\ - - Shoulder muscle weakness (in some patients)\n- Hypotrophy of the small hand muscles\n\ - - Fiber-type predominance seen on muscle biopsy (in some patients)\n- Fiber size\ - \ variation (in some patients)\n- Internal nuclei (in some patients)\n- Increased\ - \ connective tissue (in some patients)\n- Nemaline rods (in some patients)\n- Group\ - \ fiber atrophy (in some patients)\n- Angular fibers (in some patients)\n- EMG consistent\ - \ with chronic neurogenic disorder\nNEUROLOGIC\nCentral Nervous System\n- Delayed\ - \ motor development (in some patients)\nPeripheral Nervous System\n- Distal limb\ - \ muscle weakness due to peripheral neuropathy\n- Distal limb muscle atrophy due\ - \ to peripheral neuropathy\n- 'Steppage' gait\n- Foot drop\n- Distal sensory impairment\n\ - - Hyporeflexia\n- Areflexia\n- Normal or mildly decreased motor nerve conduction\ - \ velocity (NCV) (greater than 38 m/s)\n- Axonopathy seen on nerve biopsy\n- Giant\ - \ axons with accumulation of disorganized neurofilaments\nMISCELLANEOUS\n- Variable\ - \ age of onset (range first to third decade)\n- Usually begins in feet and legs\ - \ (peroneal distribution)\n- Upper limb involvement occurs later\n- Variable severity\n\ - - Some patients may become wheelchair-bound\nMOLECULAR BASIS\n- Caused by mutation\ - \ in the light polypeptide neurofilament protein gene (NEFL, 162280.0001)\n\n\n\ - ===\n\n" diff --git a/tests/output/mendelian-disease-cmt2e.pickle b/tests/output/mendelian-disease-cmt2e.pickle deleted file mode 100644 index d95ed2f1f..000000000 Binary files a/tests/output/mendelian-disease-cmt2e.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-cmt2e.yaml b/tests/output/mendelian-disease-cmt2e.yaml deleted file mode 100644 index 11186dee1..000000000 --- a/tests/output/mendelian-disease-cmt2e.yaml +++ /dev/null @@ -1,146 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-cmt2e.txt -input_text: "Mersiyanova et al. (2000) reported a large 6-generation family from Russia\ - \ with autosomal dominant CMT2. Onset was in the second and third decade, characterized\ - \ by difficulty in walking and weakness and atrophy of the distal lower limb muscles\ - \ and a variable degree of deformity of the feet (pes cavus). Affected individuals\ - \ did not exhibit enlarged nerves, ulcerated feet, hearing impairment, or paralysis\ - \ of the vocal cords. Several patients had hyperkeratosis, although the association,\ - \ if any, between the 2 disorders was not clear. The authors suggested the designation\ - \ CMT2E for this disorder. \n\nGeorgiou et al. (2002) described a large 5-generation\ - \ Slovenian family with autosomal dominant CMT type 2E. Disease onset in most patients\ - \ was in the first decade of life. The presenting symptoms were difficulty in walking\ - \ or running, due to a slowly progressive distal weakness and wasting of the lower\ - \ limbs. A steppage gait, pes cavus, and hammertoes were typically present. Over\ - \ a period of 20 years after disease onset, two-thirds of patients developed upper\ - \ limb involvement resulting in claw hands. All patients were ambulatory 20 to 30\ - \ years after onset. \n\nFabrizi et al. (2004) reported a large kindred from southern\ - \ Italy with autosomal dominant CMT2E spanning 5 generations and caused by mutation\ - \ in the NEFL gene (162280.0002). An affected woman and her 2 affected sons had\ - \ steppage gait, ataxic gait, peroneal muscular atrophy, decreased vibration sense\ - \ with stocking and glove distribution, and hypotrophy of the hand muscles. One\ - \ of the sons had claw hand deformities. Motor nerve conduction velocities (NCV)\ - \ were decreased, consistent with a demyelinating neuropathy, but sural nerve biopsy\ - \ of the mother showed a primary axonopathy characterized by giant axons containing\ - \ disorganized neurofilaments. \n\nMiltenberger-Miltenyi et al. (2007) reported\ - \ a large Austrian family in which at least 4 members had CMT2E confirmed by genetic\ - \ analysis (162880.0006). Disease onset was in the second decade of life with pes\ - \ cavus, progressive plantar extensor weakness, and distal lower limb atrophy and\ - \ weakness. Two patients became wheelchair-bound. Affected members of a second Austrian\ - \ family, with a different NEFL mutation (162280.0003), had disease onset before\ - \ age 15 years in all but 1 patient. The disorder was slowly progressive but resulted\ - \ in a severe and disabling phenotype. Electrophysiologic studies of both families\ - \ showed intermediate motor nerve conduction velocities consistent with axonal pathology.\n" -raw_completion_output: "Name: CMT2\nDescription: A hereditary motor and sensory neuropathy\ - \ characterized by slowly progressive distal lower limb muscle weakness.\nSynonyms:\ - \ Charcot-Marie-Tooth disease type 2; Hereditary Motor and Sensory Neuropathy Type\ - \ 2; CMT2E\nSubclass_of: Charcot-Marie-Tooth Disease\nSymptoms: Difficulty in walking;\ - \ Steppage gait; Pes cavus; Hammertoes; Claw hands; Decreased vibration sense with\ - \ stocking and glove distribution; Hypotrophy of hand muscles\nInheritance: Autosomal\ - \ dominant\nGenes: NEFL; 162280.0002; 162880.0006; 162280.0003\nDisease_Onsets:\ - \ Second and third decade; First decade; Adult; Juvenile; First decade \nLabel:\ - \ Charcot-Marie-Tooth Disease Type 2" -prompt: "From the text below, extract the following entities in the following format:\n\ - \nname: \ndescription: \n\ - synonyms: \nsubclass_of: \nsymptoms: \ninheritance:\ - \ \ngenes: \ndisease_onsets: \n\ - label: \n\n\nText:\nMersiyanova et al. (2000)\ - \ reported a large 6-generation family from Russia with autosomal dominant CMT2.\ - \ Onset was in the second and third decade, characterized by difficulty in walking\ - \ and weakness and atrophy of the distal lower limb muscles and a variable degree\ - \ of deformity of the feet (pes cavus). Affected individuals did not exhibit enlarged\ - \ nerves, ulcerated feet, hearing impairment, or paralysis of the vocal cords. Several\ - \ patients had hyperkeratosis, although the association, if any, between the 2 disorders\ - \ was not clear. The authors suggested the designation CMT2E for this disorder.\ - \ \n\nGeorgiou et al. (2002) described a large 5-generation Slovenian family with\ - \ autosomal dominant CMT type 2E. Disease onset in most patients was in the first\ - \ decade of life. The presenting symptoms were difficulty in walking or running,\ - \ due to a slowly progressive distal weakness and wasting of the lower limbs. A\ - \ steppage gait, pes cavus, and hammertoes were typically present. Over a period\ - \ of 20 years after disease onset, two-thirds of patients developed upper limb involvement\ - \ resulting in claw hands. All patients were ambulatory 20 to 30 years after onset.\ - \ \n\nFabrizi et al. (2004) reported a large kindred from southern Italy with autosomal\ - \ dominant CMT2E spanning 5 generations and caused by mutation in the NEFL gene\ - \ (162280.0002). An affected woman and her 2 affected sons had steppage gait, ataxic\ - \ gait, peroneal muscular atrophy, decreased vibration sense with stocking and glove\ - \ distribution, and hypotrophy of the hand muscles. One of the sons had claw hand\ - \ deformities. Motor nerve conduction velocities (NCV) were decreased, consistent\ - \ with a demyelinating neuropathy, but sural nerve biopsy of the mother showed a\ - \ primary axonopathy characterized by giant axons containing disorganized neurofilaments.\ - \ \n\nMiltenberger-Miltenyi et al. (2007) reported a large Austrian family in which\ - \ at least 4 members had CMT2E confirmed by genetic analysis (162880.0006). Disease\ - \ onset was in the second decade of life with pes cavus, progressive plantar extensor\ - \ weakness, and distal lower limb atrophy and weakness. Two patients became wheelchair-bound.\ - \ Affected members of a second Austrian family, with a different NEFL mutation (162280.0003),\ - \ had disease onset before age 15 years in all but 1 patient. The disorder was slowly\ - \ progressive but resulted in a severe and disabling phenotype. Electrophysiologic\ - \ studies of both families showed intermediate motor nerve conduction velocities\ - \ consistent with axonal pathology.\n\n\n===\n\n" -extracted_object: - label: Charcot-Marie-Tooth Disease Type 2 - name: CMT2 - description: A hereditary motor and sensory neuropathy characterized by slowly progressive - distal lower limb muscle weakness. - synonyms: - - Charcot-Marie-Tooth disease type 2 - - Hereditary Motor and Sensory Neuropathy Type 2 - - CMT2E - subclass_of: - - MONDO:0015626 - symptoms: - - HP:0002355 - - HP:0003376 - - HP:0001761 - - HP:0001765 - - AUTO:Claw%20hands - - AUTO:Decreased%20vibration%20sense%20with%20stocking%20and%20glove%20distribution - - AUTO:Hypotrophy%20of%20hand%20muscles - inheritance: HP:0000006 - genes: - - HGNC:7739 - - AUTO:162280.0002 - - AUTO:162880.0006 - - AUTO:162280.0003 - disease_onsets: - - AUTO:Second%20and%20third%20decade - - AUTO:First%20decade - - AUTO:Adult - - AUTO:Juvenile - - AUTO:First%20decade -named_entities: -- id: MONDO:0015626 - label: Charcot-Marie-Tooth Disease -- id: HP:0002355 - label: Difficulty in walking -- id: HP:0003376 - label: Steppage gait -- id: HP:0001761 - label: Pes cavus -- id: HP:0001765 - label: Hammertoes -- id: AUTO:Claw%20hands - label: Claw hands -- id: AUTO:Decreased%20vibration%20sense%20with%20stocking%20and%20glove%20distribution - label: Decreased vibration sense with stocking and glove distribution -- id: AUTO:Hypotrophy%20of%20hand%20muscles - label: Hypotrophy of hand muscles -- id: HP:0000006 - label: Autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: AUTO:162280.0002 - label: '162280.0002' -- id: AUTO:162880.0006 - label: '162880.0006' -- id: AUTO:162280.0003 - label: '162280.0003' -- id: AUTO:Second%20and%20third%20decade - label: Second and third decade -- id: AUTO:First%20decade - label: First decade -- id: AUTO:Adult - label: Adult -- id: AUTO:Juvenile - label: Juvenile diff --git a/tests/output/mendelian-disease-marfan.pickle b/tests/output/mendelian-disease-marfan.pickle deleted file mode 100644 index 94541bc43..000000000 Binary files a/tests/output/mendelian-disease-marfan.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-marfan.yaml b/tests/output/mendelian-disease-marfan.yaml deleted file mode 100644 index c4bd19191..000000000 --- a/tests/output/mendelian-disease-marfan.yaml +++ /dev/null @@ -1,159 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-marfan.txt -input_text: Marfan syndrome is a genetic disorder that affects connective tissue, - which is the material between cells of the body that gives the tissues form and - strength. Connective tissue is found all over the body and multiple organ systems - may be affected in individuals with Marfan syndrome. The heart and blood vessels - (cardiovascular), skeletal, and eye (ocular) systems are most often affected. Major - symptoms include overgrowth of the long bones of the arms and legs, abnormal side-to-side - curvature of the spine (scoliosis), indentation or protrusion of the chest wall - (pectus deformity), dislocation of the lenses of the eyes (ectopia lentis), nearsightedness - (myopia), widening (aneurysm) and tear (dissection) of the main artery that carries - blood away from the heart (aorta), floppiness of the mitral valve (mitral valve - prolapse) and backward flow of blood through the aortic and mitral valves (aortic - and mitral regurgitation). The specific symptoms and the severity of Marfan syndrome - vary greatly from person to person. Marfan syndrome is inherited as an autosomal - dominant trait, meaning that only one abnormal copy of the Marfan gene inherited - from one parent is sufficient to have the condition. Defects or deletions (pathogenic - variants) of the fibrillin-1 (FBN1) gene have been shown to cause Marfan syndrome. -raw_completion_output: "Name: Marfan syndrome \nDescription: A genetic disorder that\ - \ affects connective tissue, which is the material between cells of the body that\ - \ gives the tissues form and strength \nSynonyms: Marfan\u2019s Syndrome; Marie\u2013\ - Strumpell disease; Ochronotic arthropathy; Dysfibrillinosis \nSubclass_of: N/A\n\ - Symptoms: Overgrowth of the long bones of the arms and legs; abnormal side-to-side\ - \ curvature of the spine (scoliosis); indentation or protrusion of the chest wall\ - \ (pectus deformity); dislocation of the lenses of the eyes (ectopia lentis); nearsightedness\ - \ (myopia); widening (aneurysm); tear (dissection) of the main artery that carries\ - \ blood away from the heart (aorta); floppiness of the mitral valve (mitral valve\ - \ prolapse); backward flow of blood through the aortic and mitral valves (aortic\ - \ and mitral regurgitation)\nInheritance: Autosomal Dominant \nGenes: FBN1 \nDisease_Onsets:\ - \ Adult; Juvenile; First Decade \nLabel: Marfan Syndrome" -prompt: 'From the text below, extract the following entities in the following format: - - - name: - - description: - - synonyms: - - subclass_of: - - symptoms: - - inheritance: - - genes: - - disease_onsets: - - label: - - - - Text: - - Marfan syndrome is a genetic disorder that affects connective tissue, which is the - material between cells of the body that gives the tissues form and strength. Connective - tissue is found all over the body and multiple organ systems may be affected in - individuals with Marfan syndrome. The heart and blood vessels (cardiovascular), - skeletal, and eye (ocular) systems are most often affected. Major symptoms include - overgrowth of the long bones of the arms and legs, abnormal side-to-side curvature - of the spine (scoliosis), indentation or protrusion of the chest wall (pectus deformity), - dislocation of the lenses of the eyes (ectopia lentis), nearsightedness (myopia), - widening (aneurysm) and tear (dissection) of the main artery that carries blood - away from the heart (aorta), floppiness of the mitral valve (mitral valve prolapse) - and backward flow of blood through the aortic and mitral valves (aortic and mitral - regurgitation). The specific symptoms and the severity of Marfan syndrome vary greatly - from person to person. Marfan syndrome is inherited as an autosomal dominant trait, - meaning that only one abnormal copy of the Marfan gene inherited from one parent - is sufficient to have the condition. Defects or deletions (pathogenic variants) - of the fibrillin-1 (FBN1) gene have been shown to cause Marfan syndrome. - - - === - - - ' -extracted_object: - label: Marfan Syndrome - name: Marfan syndrome - description: A genetic disorder that affects connective tissue, which is the material - between cells of the body that gives the tissues form and strength - synonyms: - - "Marfan\u2019s Syndrome" - - "Marie\u2013Strumpell disease" - - Ochronotic arthropathy - - Dysfibrillinosis - subclass_of: - - AUTO:N/A - symptoms: - - AUTO:Overgrowth%20of%20the%20long%20bones%20of%20the%20arms%20and%20legs - - AUTO:abnormal%20side-to-side%20curvature%20of%20the%20spine%20%28scoliosis%29 - - AUTO:indentation%20or%20protrusion%20of%20the%20chest%20wall%20%28pectus%20deformity%29 - - AUTO:dislocation%20of%20the%20lenses%20of%20the%20eyes%20%28ectopia%20lentis%29 - - AUTO:nearsightedness%20%28myopia%29 - - AUTO:widening%20%28aneurysm%29 - - AUTO:tear%20%28dissection%29%20of%20the%20main%20artery%20that%20carries%20blood%20away%20from%20the%20heart%20%28aorta%29 - - AUTO:floppiness%20of%20the%20mitral%20valve%20%28mitral%20valve%20prolapse%29 - - AUTO:backward%20flow%20of%20blood%20through%20the%20aortic%20and%20mitral%20valves%20%28aortic%20and%20mitral%20regurgitation%29 - inheritance: HP:0000006 - genes: - - HGNC:3603 - disease_onsets: - - AUTO:Adult - - AUTO:Juvenile - - AUTO:First%20Decade -named_entities: -- id: HP:0009830 - label: Peripheral Neuropathy -- id: HP:0001371 - label: Joint contractures -- id: HP:0001761 - label: Pes cavus -- id: HP:0001760 - label: Foot deformities -- id: HP:0006006 - label: Hypotrophy of the small hand muscles -- id: HP:0002460 - label: Distal limb muscle weakness due to peripheral neuropathy -- id: HP:0009027 - label: Foot drop -- id: HP:0002936 - label: Distal sensory impairment -- id: HP:0001265 - label: Hyporeflexia -- id: HP:0001284 - label: Areflexia -- id: HP:0000006 - label: Autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: MONDO:0030433 - label: Charcot-Marie-Tooth Neuropathy -- id: MONDO:0015626 - label: Peroneal Muscular Atrophy -- id: HP:0003376 - label: steppage gait -- id: HP:0001761 - label: pes cavus -- id: HP:0001765 - label: hammertoes -- id: HP:0000006 - label: autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: HGNC:8850 - label: PEX1 -- id: HGNC:9717 - label: PEX2 -- id: HGNC:8858 - label: PEX3 -- id: HP:0000007 - label: Autosomal recessive -- id: HGNC:4696 - label: "\u03B2-glucuronidase" -- id: HP:0000006 - label: Autosomal Dominant -- id: HGNC:3603 - label: FBN1 diff --git a/tests/output/mendelian-disease-sly.pickle b/tests/output/mendelian-disease-sly.pickle deleted file mode 100644 index b12c4fa03..000000000 Binary files a/tests/output/mendelian-disease-sly.pickle and /dev/null differ diff --git a/tests/output/mendelian-disease-sly.yaml b/tests/output/mendelian-disease-sly.yaml deleted file mode 100644 index e2040fd59..000000000 --- a/tests/output/mendelian-disease-sly.yaml +++ /dev/null @@ -1,92 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/mendelian-disease-sly.txt -input_text: "Sly syndrome, also called mucopolysaccharidosis type VII (MPS-VII), is\ - \ an autosomal recessive lysosomal storage disease caused by a deficiency of the\ - \ enzyme \u03B2-glucuronidase. This enzyme is responsible for breaking down large\ - \ sugar molecules called glycosaminoglycans (AKA GAGs, or mucopolysaccharides).\ - \ The inability to break down GAGs leads to a buildup in many tissues and organs\ - \ of the body. The severity of the disease can vary widely.\n" -raw_completion_output: "Name: Sly Syndrome\nDescription: Autosomal recessive lysosomal\ - \ storage disease caused by a deficiency of the enzyme \u03B2-glucuronidase\nSynonyms:\ - \ Mucopolysaccharidosis type VII (MPS-VII)\nSubclass_of: None\nSymptoms: Buildup\ - \ in many tissues and organs of the body, Severity of the disease can vary widely\n\ - Inheritance: Autosomal recessive\nGenes: \u03B2-glucuronidase \nDisease_Onsets:\ - \ None\nLabel: Sly Syndrome" -prompt: "From the text below, extract the following entities in the following format:\n\ - \nname: \ndescription: \n\ - synonyms: \nsubclass_of: \nsymptoms: \ninheritance:\ - \ \ngenes: \ndisease_onsets: \n\ - label: \n\n\nText:\nSly syndrome, also called\ - \ mucopolysaccharidosis type VII (MPS-VII), is an autosomal recessive lysosomal\ - \ storage disease caused by a deficiency of the enzyme \u03B2-glucuronidase. This\ - \ enzyme is responsible for breaking down large sugar molecules called glycosaminoglycans\ - \ (AKA GAGs, or mucopolysaccharides). The inability to break down GAGs leads to\ - \ a buildup in many tissues and organs of the body. The severity of the disease\ - \ can vary widely.\n\n\n===\n\n" -extracted_object: - label: Sly Syndrome - name: Sly Syndrome - description: "Autosomal recessive lysosomal storage disease caused by a deficiency\ - \ of the enzyme \u03B2-glucuronidase" - synonyms: - - Mucopolysaccharidosis type VII (MPS-VII) - subclass_of: - - AUTO:None - symptoms: - - AUTO:Buildup%20in%20many%20tissues%20and%20organs%20of%20the%20body%2C%20Severity%20of%20the%20disease%20can%20vary%20widely - inheritance: HP:0000007 - genes: - - HGNC:4696 - disease_onsets: - - AUTO:None -named_entities: -- id: HP:0009830 - label: Peripheral Neuropathy -- id: HP:0001371 - label: Joint contractures -- id: HP:0001761 - label: Pes cavus -- id: HP:0001760 - label: Foot deformities -- id: HP:0006006 - label: Hypotrophy of the small hand muscles -- id: HP:0002460 - label: Distal limb muscle weakness due to peripheral neuropathy -- id: HP:0009027 - label: Foot drop -- id: HP:0002936 - label: Distal sensory impairment -- id: HP:0001265 - label: Hyporeflexia -- id: HP:0001284 - label: Areflexia -- id: HP:0000006 - label: Autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: MONDO:0030433 - label: Charcot-Marie-Tooth Neuropathy -- id: MONDO:0015626 - label: Peroneal Muscular Atrophy -- id: HP:0003376 - label: steppage gait -- id: HP:0001761 - label: pes cavus -- id: HP:0001765 - label: hammertoes -- id: HP:0000006 - label: autosomal dominant -- id: HGNC:7739 - label: NEFL -- id: HGNC:8850 - label: PEX1 -- id: HGNC:9717 - label: PEX2 -- id: HGNC:8858 - label: PEX3 -- id: HP:0000007 - label: Autosomal recessive -- id: HGNC:4696 - label: "\u03B2-glucuronidase" diff --git a/tests/output/owl/merged/recipe-all-merged.owl b/tests/output/owl/merged/recipe-all-merged.owl deleted file mode 100644 index bec3952d9..000000000 --- a/tests/output/owl/merged/recipe-all-merged.owl +++ /dev/null @@ -1,54490 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - a core relation that holds between a part and its whole - - part of - part of - part_of - - - - - - - - - - has part - a core relation that holds between a whole and its part - - - has part - has part - has_part - - - - - - - - - has food substance analog - - - - - - - - - A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. - Damion Dooley - FoodOn - For example, 'bean soup' has a defining ingredient of some 'bean (whole)'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. - -A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. - has defining ingredient - - - - - - - - - - - A relation attaching between a food material and another food material that has been added to it at some point in its history. - Damion Dooley - FoodOn - has ingredient - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_of - - has_specified_output - - - - - - - - participates in - a relation between a continuant and a process, in which the continuant is somehow involved in the process - - - participates in - participates_in - - - - - - - - has participant - a relation between a process and a continuant, in which the continuant is somehow involved in the process - - has participant - has_participant - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - - has quality - - - - - - - - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - - has role - - - - - - - - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - - derives from - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - in taxon - - - - - - - - - develops from - develops from - develops_from - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - has input - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - has output - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - - member of - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - inverse of has output - - output of - - - - - - - - x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - composed primarily of - - - - - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - - produced by - - - - - - - - - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - Damion Dooley - - has substance added - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Place - - - - - - - - - Add - - - - - - - - - Bacon - - - - - - - - - Bowl - - - - - - - - - Can - - - - - - - - - Cilantro - - - - - - - - - Combine - - - - - - - - - Cook - - - - - - - - - Cool - - - - - - - - - Cooled - - - - - - - - - Dip - - - - - - - - - Drain - - - - - - - - - Drizzle - - - - - - - - - Form - - - - - - - - - Fry - - - - - - - - - Golden - - - - - - - - - Heat - - - - - - - - - Insert - - - - - - - - - Knife. - - - - - - - - - Mix - - - - - - - - - Mixture - - - - - - - - - NA - - - - - - - - - None - - - - - - - - - None. - - - - - - - - - Oven - - - - - - - - - Pan - - - - - - - - - Paprika - - - - - - - - - Pot - - - - - - - - - Pour - - - - - - - - - Preheat - - - - - - - - - Repeat - - - - - - - - - Return - - - - - - - - - Ricotta - - - - - - - - - Salt - - - - - - - - - Saute - - - - - - - - - Serve - - - - - - - - - Simmer - - - - - - - - - Soup - - - - - - - - - Spoon - - - - - - - - - Spray - - - - - - - - - Stir - - - - - - - - - Tbsp - - - - - - - - - Tbsp. - - - - - - - - - Transfer - - - - - - - - - Well - - - - - - - - - Whisk - - - - - - - - - a - - - - - - - - - add - - - - - - - - - bacon - - - - - - - - - blender - - - - - - - - - bowl - - - - - - - - - bowl. - - - - - - - - - bread - - - - - - - - - brioche - - - - - - - - - bunch - - - - - - - - - buttermilk - - - - - - - - - cayenne - - - - - - - - - charred - - - - - - - - - chilies - - - - - - - - - chill - - - - - - - - - chopped - - - - - - - - - cilantro - - - - - - - - - colander - - - - - - - - - combine - - - - - - - - - cook - - - - - - - - - coriander - - - - - - - - - corn - - - - - - - - - cornstarch - - - - - - - - - covered - - - - - - - - - crisp - - - - - - - - - cup - - - - - - - - - cups - - - - - - - - - diced - - - - - - - - - dry - - - - - - - - - feta - - - - - - - - - first - - - - - - - - - fork - - - - - - - - - fork. - - - - - - - - - fragrant - - - - - - - - - g - - - - - - - - - golden - - - - - - - - - grill. - - - - - - - - - hands. - - - - - - - - - heat - - - - - - - - - iron - - - - - - - - - knife. - - - - - - - - - large - - - - - - - - - lbs - - - - - - - - - meat - - - - - - - - - medium - - - - - - - - - minced - - - - - - - - - mix - - - - - - - - - mixture - - - - - - - - - mustard - - - - - - - - - none - - - - - - - - - none. - - - - - - - - - oz - - - - - - - - - pan - - - - - - - - - pan. - - - - - - - - - pieces - - - - - - - - - pinch - - - - - - - - - plate - - - - - - - - - platter - - - - - - - - - pot - - - - - - - - - pot. - - - - - - - - - remove - - - - - - - - - ribbons - - - - - - - - - rolling - - - - - - - - - room - - - - - - - - - salt - - - - - - - - - saucepan - - - - - - - - - saucepan. - - - - - - - - - serve - - - - - - - - - simmer - - - - - - - - - skillet - - - - - - - - - skillet. - - - - - - - - - sliced - - - - - - - - - small - - - - - - - - - smock - - - - - - - - - smooth - - - - - - - - - soup - - - - - - - - - spoon - - - - - - - - - sticks - - - - - - - - - stir - - - - - - - - - stir-fry - - - - - - - - - stove - - - - - - - - - thermometer - - - - - - - - - thick - - - - - - - - - to - - - - - - - - - tsp - - - - - - - - - tsp. - - - - - - - - - whisk - - - - - - - - - whisk. - - - - - - - - - wok - - - - - - - - - (15 ounce) cans - - - - - - - - - <N/A> - - - - - - - - - - - - - - - - - - - 1 cup - - - - - - - - - 1 (15 oz) can fire roasted tomatoes - - - - - - - - - 1 (16 ounce) box spaghetti noodles - - - - - - - - - 1 (4 oz) can green chilies - - - - - - - - - 1 large egg - - - - - - - - - 1/2 cup soy sauce - - - - - - - - - 10 ounce packages - - - - - - - - - 2 large eggs - - - - - - - - - 3 to 5 minutes - - - - - - - - - 300° - - - - - - - - - Add; - - - - - - - - - Add; Continue cooking - - - - - - - - - Add; stir fry - - - - - - - - - Baking sheet. - - - - - - - - - Beat; incorporate - - - - - - - - - Boil; Drain - - - - - - - - - Boiled Water - - - - - - - - - Chopped fresh chives - - - - - - - - - Cook; Stir - - - - - - - - - Cook; stir - - - - - - - - - Cover; Chill - - - - - - - - - Crushed red pepper flakes - - - - - - - - - Cut; - - - - - - - - - Dijon mustard - - - - - - - - - Dip; press - - - - - - - - - Discarded ribs - - - - - - - - - Do Ahead - - - - - - - - - Drizzle; Add - - - - - - - - - Fill; pipe - - - - - - - - - Flaky sea salt - - - - - - - - - Freshly ground black pepper - - - - - - - - - Fried corn dogs - - - - - - - - - Gather; - - - - - - - - - Good Olive Oil - - - - - - - - - Heat; - - - - - - - - - Hot dish - - - - - - - - - Immersion blender - - - - - - - - - Insert; - - - - - - - - - Large eggs - - - - - - - - - Let sit - - - - - - - - - Make; let - - - - - - - - - Melt; Sauté - - - - - - - - - Mix; - - - - - - - - - N/A - - - - - - - - - N/A. - - - - - - - - - Pastry bag - - - - - - - - - Peel; Halve - - - - - - - - - Pick; - - - - - - - - - Place; - - - - - - - - - Pour; - - - - - - - - - Preheat; - - - - - - - - - Purée; add - - - - - - - - - Puréed soup - - - - - - - - - Read; - - - - - - - - - Red onion - - - - - - - - - Red Delicious apple - - - - - - - - - Red wine vinegar - - - - - - - - - Remove from heat - - - - - - - - - Remove; Cool - - - - - - - - - Serve; - - - - - - - - - Serving dish - - - - - - - - - Set up - - - - - - - - - Shredded Cheddar cheese - - - - - - - - - Slice; Place - - - - - - - - - Spread; - - - - - - - - - Stir; - - - - - - - - - Stir; sauté - - - - - - - - - Thai chilies - - - - - - - - - Toasted country-style bread - - - - - - - - - Toss; - - - - - - - - - Toss; Serve - - - - - - - - - Transfer; Cover - - - - - - - - - Wilted Kale - - - - - - - - - Work surface - - - - - - - - - Wrap; Chill - - - - - - - - - add; - - - - - - - - - add; cook - - - - - - - - - add; mix - - - - - - - - - add; stir - - - - - - - - - add; sauté - - - - - - - - - adjust; - - - - - - - - - all-purpose flour - - - - - - - - - apple cider vinegar - - - - - - - - - asparagus spears - - - - - - - - - bacon drippings - - - - - - - - - baking soda - - - - - - - - - bay leaves - - - - - - - - - blanched hazelnuts - - - - - - - - - blended mixture - - - - - - - - - both sides - - - - - - - - - bottom of the pan - - - - - - - - - bring to a rolling boil - - - - - - - - - bring to a simmer; - - - - - - - - - bring; - - - - - - - - - caramelized sauce - - - - - - - - - cayenne pepper - - - - - - - - - cloves garlic - - - - - - - - - coat; - - - - - - - - - coated noodles - - - - - - - - - cold water - - - - - - - - - combined mixture - - - - - - - - - cook and stir; - - - - - - - - - cook; - - - - - - - - - cook; stir - - - - - - - - - cooking spray - - - - - - - - - covered pan - - - - - - - - - creamed corn - - - - - - - - - crushed red pepper - - - - - - - - - crushed red pepper flakes - - - - - - - - - cubed paneer - - - - - - - - - cut; toss - - - - - - - - - cutting board - - - - - - - - - divide; roll out - - - - - - - - - drizzle; sprinkle - - - - - - - - - dry Chinese noodles - - - - - - - - - dry hot dogs - - - - - - - - - extra-virgin olive oil - - - - - - - - - food processor - - - - - - - - - fresh ricotta - - - - - - - - - fresh basil leaves - - - - - - - - - fresh ginger root - - - - - - - - - fresh lime juice - - - - - - - - - freshly ground black pepper - - - - - - - - - frozen chopped spinach - - - - - - - - - garam masala - - - - - - - - - garlic cloves - - - - - - - - - glazed meat - - - - - - - - - granulated sugar - - - - - - - - - grated fresh ginger root - - - - - - - - - ground coriander - - - - - - - - - ground cumin - - - - - - - - - ground turmeric - - - - - - - - - heat; - - - - - - - - - heated cooking oil - - - - - - - - - hot chile pepper - - - - - - - - - hot cooked rice - - - - - - - - - inch thick pieces - - - - - - - - - jumbo or regular - - - - - - - - - knead; - - - - - - - - - kosher salt - - - - - - - - - large carrot - - - - - - - - - large pot - - - - - - - - - large saucepan - - - - - - - - - large skillet - - - - - - - - - large leaves of lettuce - - - - - - - - - large stock pot - - - - - - - - - large, chopped - - - - - - - - - large, sliced - - - - - - - - - large, deep skillet - - - - - - - - - lemon, more to taste - - - - - - - - - let cool; - - - - - - - - - let sit; - - - - - - - - - let stand; - - - - - - - - - lift; add - - - - - - - - - mash; - - - - - - - - - medium, sliced into 1/4-inch half circles - - - - - - - - - mint sprigs - - - - - - - - - mix; - - - - - - - - - mixed ingredients - - - - - - - - - n/a - - - - - - - - - napa cabbage - - - - - - - - - none; - - - - - - - - - outdoor grill - - - - - - - - - paper towels. - - - - - - - - - pastry bag - - - - - - - - - pat; dust - - - - - - - - - peanut or vegetable oil - - - - - - - - - peeled and diced - - - - - - - - - place; - - - - - - - - - pluck out - - - - - - - - - plumped raisins - - - - - - - - - poached chicken - - - - - - - - - popsicle sticks - - - - - - - - - pre-cooked chicken - - - - - - - - - preheat; - - - - - - - - - quick-cooking grits - - - - - - - - - red enchilada sauce - - - - - - - - - red pepper flakes - - - - - - - - - red wine vinegar - - - - - - - - - reduce; add - - - - - - - - - reduce; stir; simmer - - - - - - - - - regular blender - - - - - - - - - reserved dressing - - - - - - - - - return to a boil; - - - - - - - - - rimmed baking sheet - - - - - - - - - sauce mixture - - - - - - - - - scatter; - - - - - - - - - sea salt - - - - - - - - - season; - - - - - - - - - serve; - - - - - - - - - set aside - - - - - - - - - skinless, boneless chicken thighs - - - - - - - - - slice; - - - - - - - - - sliced carrots - - - - - - - - - slotted spatula - - - - - - - - - slotted spoon. - - - - - - - - - slotted spoon, bowl - - - - - - - - - small bowl - - - - - - - - - small (chopped) - - - - - - - - - small bunch mint - - - - - - - - - soak; - - - - - - - - - soft lentils - - - - - - - - - spread; - - - - - - - - - stir; - - - - - - - - - stirring utensil. - - - - - - - - - sweet chili sauce - - - - - - - - - tablespoons, plus more for drizzling - - - - - - - - - tastier dish - - - - - - - - - top; dress - - - - - - - - - topping; - - - - - - - - - toss and saute; - - - - - - - - - toss; - - - - - - - - - transfer; - - - - - - - - - transfer; blend - - - - - - - - - two salads - - - - - - - - - two large plates - - - - - - - - - two pieces of dough - - - - - - - - - uncooked medium shrimp - - - - - - - - - vanilla extract - - - - - - - - - waffle iron - - - - - - - - - waffle iron. - - - - - - - - - well done - - - - - - - - - whisk; - - - - - - - - - white wine vinegar - - - - - - - - - yellow cornmeal - - - - - - - - - yolk mixture - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - continuant - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - material - MaterialEntity - material entity - material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - bfo - BFO:0000040 - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - A peduncle arising at or beneath the surface of the ground in an acaulescent plant (as the tulip); broadly: a flower stalk. - - BrendaTissueOBO - BTO:0001217 - scape - - - - - - - - - A material entity that is ingested and contributes to survival, growth and development - - dietary chemical component - - - - - - - - - Carbohydrates that are absorbed in the small intestine and provide carbohydrate for metabolism in monogastric animals. - - digestible carbohydrate - available carbohydrate - - - - - - - - - Available carbohydrate in monosaccharide and disaccharide form - - free sugar - - - - - - - - - - - Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. - - - CHEBI:15131 - CHEBI:23008 - CHEBI:9318 - Wikipedia:Carbohydrate - carbohydrate - carbohydrates - chebi_ontology - Kohlenhydrat - Kohlenhydrate - a carbohydrate - carbohidrato - carbohidratos - glucide - glucides - glucido - glucidos - hydrates de carbone - saccharide - saccharides - saccharidum - CHEBI:16646 - - carbohydrate - carbohydrate - - - - - - - - - Any oligosaccharide, polysaccharide or their derivatives consisting of monosaccharides or monosaccharide derivatives linked by glycosidic bonds. See also http://www.ontobee.org/ontology/GNO?iri=http://purl.obolibrary.org/obo/GNO_00000001. - - glycan - - - - - - - - - - - A glycosyl glycoside formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. - - - 0 - C12H22O11 - InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 - CZMRCDWAGMRECN-UGDNZRGBSA-N - 342.29650 - 342.11621 - OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O - CHEBI:15128 - CHEBI:26812 - CHEBI:45795 - CHEBI:9314 - Beilstein:90825 - CAS:57-50-1 - DrugBank:DB02772 - Drug_Central:4610 - Gmelin:97695 - HMDB:HMDB0000258 - KEGG:C00089 - KEGG:D00025 - KEGG:D06533 - KEGG:G00370 - KNApSAcK:C00001151 - MetaCyc:SUCROSE - PDBeChem:SUC - PMID:11021636 - PMID:11093712 - PMID:11111003 - PMID:12065720 - PMID:12706980 - PMID:13508893 - PMID:15291457 - PMID:15660210 - PMID:15792978 - PMID:15845855 - PMID:16228482 - PMID:16304615 - PMID:16313996 - PMID:16525719 - PMID:16660545 - PMID:16663947 - PMID:16665852 - PMID:17233733 - PMID:17439666 - PMID:17597061 - PMID:18625236 - PMID:19199566 - PMID:19726178 - PMID:21703290 - PMID:21972845 - PMID:22085755 - PMID:22311778 - PMID:22404833 - PMID:22751876 - Reaxys:1435311 - Reaxys:90825 - SUBSET_SIREN:F15176 - Wikipedia:Sucrose - http://www.langual.org/langual_thesaurus.asp?termid=C0210 - http://www.langual.org/langual_thesaurus.asp?termid=H0136 - http://www.langual.org/langual_thesaurus.asp?termid=H0158 - SUCROSE - Sucrose - beta-D-fructofuranosyl alpha-D-glucopyranoside - sucrose - chebi_ontology - 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside - Cane sugar - Saccharose - Sacharose - White sugar - beta-D-Fruf-(2<->1)-alpha-D-Glcp - sacarosa - table sugar - CHEBI:17992 - - subset_siren - LanguaL term definition: Used when sucrose (e.g., cane sugar or beet sugar) is the major ingredient. Note: on a product label or in a recipe, 'sugar' means sucrose. - sucrose - sucrose - - - - - - - - - - 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. - - - CHEBI:14517 - CHEBI:25054 - CHEBI:6486 - KEGG:C01356 - Lipid - lipids - chebi_ontology - CHEBI:18059 - - lipid - - - - - - - - - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - - molecular entity - - - - - - - - - Any disaccharide in which the two monosaccharide components are connected by a glycosidic linkage between their anomeric centres. - - glycosyl glycoside - - - - - - - - - A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. - - chemical entity - - - - - - - - - A role played by the molecular entity or part thereof within a biological context. - - biological role - - - - - - - - - - oxygen molecular entity - - - - - - - - - A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. - - heteroorganic entity - - - - - - - - - food role - A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. - - food - - - - - - - - - Any p-block molecular entity containing a chalcogen. - - chalcogen molecular entity - - - - - - - - - A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. - - main group molecular entity - - - - - - - - - - carbon group molecular entity - - - - - - - - - A main group molecular entity that contains one or more atoms of a p-block element. - - p-block molecular entity - - - - - - - - - A compound in which two monosaccharides are joined by a glycosidic bond. - - - CHEBI:23844 - CHEBI:4654 - KEGG:C01911 - Disaccharide - disaccharides - chebi_ontology - Disaccharid - Disacharid - disacarido - disacaridos - CHEBI:36233 - - disaccharide - disaccharide - - - - - - - - - - An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. - - organochalcogen compound - - - - - - - - - - An organochalcogen compound containing at least one carbon-oxygen bond. - - organooxygen compound - - - - - - - - - - A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. - oligosaccharide - - - http://langual.org - CHEBI:25679 - CHEBI:35319 - CHEBI:7758 - KEGG:C00930 - http://www.langual.org/langual_thesaurus.asp?termid=C0226 - Oligosaccharide - oligosaccharides - chebi_ontology - O-glycosylglycoside - O-glycosylglycosides - oligosacarido - oligosacaridos - CHEBI:50699 - - LanguaL term definition: Complex carbohydrate with molecules composed of three to ten saccharide units (specifically dextrin). May be slightly sweet to the taste. - oligosaccharide - - - - - - - - - Any molecular entity that contains carbon. - - organic molecular entity - - - - - - - - - role (CHEBI) - A role is particular behaviour which a material entity may exhibit. - - role - - - - - - - - - - physiological role - - - - - - - - - A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. - - chemical substance - - - - - - - - - A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. - - mixture - - - - - - - - - Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. - - carbohydrates and carbohydrate derivatives - - - - - - - - - - - - - - - - - - A mixture of sugar (fructose, glucose, sucrose) and carbohydrate components that is a by-product from sugar refinery. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0156 - LANGUAL:C0207 - LanguaL term definition: Liquid product remaining after crystallization of sugar from sugar syrup; most molasses is made from sugar cane. - molasses - - - - - - - - - An environmental material primarily composed of dihydrogen oxide in its liquid form. - - liquid water - - - - - - - - - Water which has a low concentration of dissolved solutes, particularly that of sodium chloride. - - fresh water - - - - - - - - - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. - - environmental - environmental material - - - - - - - - - An environmental material which is in a liquid state. - - liquid environmental material - - - - - - - - - A liquid or a gas. - - fluid environmental material - - - - - - - - - A process of cutting food into smaller pieces, chunks or slices. - Damion Dooley - food cutting process - - - - - - - - - Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. - Damion Dooley - Foodon product type - https://en.wikipedia.org/wiki/Food - The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations. - food product - - - - - - - - - - - - - - - - - - - - - - A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. - - SUBSET_SIREN:F17332 - mammalian meat food product - - - - - - - - - A processed meat food product that is made from a sausage. - - 2022-10-28T11:02:42Z - sausage food product - - - - - - - - - - A hot dog is a moist sausage of soft, even texture and flavor, often made from advanced meat recovery or meat slurry. Most types are fully cooked, cured or smoked. It is often placed hot in a special purpose soft, sliced hot dog bun. - Damion Dooley - - - hotdog - frankfurter - hot dog - hot dogs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - processed meat food product - - - - - - - - - - - - - - - - Cheese is a food derived from milk that is produced in a wide range of flavors, textures, and forms by coagulation of the milk protein casein. - SUBSET_SIREN:F1076 - https://en.wikipedia.org/wiki/Cheese - cheese - cheese - cheese food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This class includes food products which are derived from or produced by a plant. - plant food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa). - Damion Dooley - http://en.wikipedia.org/wiki/Pork - pork - Pork - pork meat food product - - - - - - - - - - - - - - - - - - - - - - - - - chicken meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - Meat from bovines, especially domestic cattle (cows). - beef food product - - - - - Meat from bovines, especially domestic cattle (cows). - http://en.wikipedia.org/wiki/Beef - - - - - - - - - - - - - - - - A seafood product is a vertebrate or invertibrate organism from an aquatic environment. - Some of the subclasses are currently freshwater organisms. - Damion Dooley - animal seafood product - - - - - - - - - - - - - - - - - - fermented dairy food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fermented fish or seafood food product - - - - - - - - - - sea water fish food product - - - - - - - - - A fine powder made from cereals or other starchy food sources. - Damion Dooley - Wikipedia:Flour - http://www.langual.org/langual_thesaurus.asp?termid=H0152 - flour added - flour food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product derived from plant fruit. - plant fruit food product - - - - - - - - - - - - - - - - - - - Apple juice is a fruit juice made by the maceration and pressing of an apple. - https://en.wikipedia.org/wiki/Apple_juice - http://langual.org - SUBSET_SIREN:F1419 - apple juice - subset_siren - apple juice - - - - - - - - - - - - - - - - - - - - - - - - - - fermented fruit food product - - - - - - - - - - - - - - - - A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid. - vinegar food product - - - - - A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid. - Wikipedia:Vinegar - - - - - - - - - - - - - - - - - - - - - - - - - - - A food preserved by soaking and storing it in vinegar or brine. - - SUBSET_SIREN:F1302 - SUBSET_SIREN:F16510 - pickled - subset_siren - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) - food (pickled) - - - - - - - - - - - - - - - - - - - - - - - - - - sugar condiment - - - - - - - - - - - A lipid material derived from plants. Physically, oils are liquid at room temperature. - Damion Dooley - - vegetable oil food product - - - - - - - - - - - - - - - - - - - - - corn flour food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product which is derived from or produced by an animal that has a vertibrae. - Damion Dooley - vertebrate animal food product - - - - - - - - - - - - - - - - - - - - - - - - - - cereal grain food product - - - - - - - - - - - - - - - - - - Damion Dooley - http://langual.org - 2019-06-11T07:25:19Z - SUBSET_SIREN:F5644 - alcoholic beverage - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) - - fermented beverage - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from an avian egg. - avian egg food product - - - - - - - - - bovine dairy food product - - - - - - - - - - - - - - - cattle dairy food product - - - - - - - - - bovine cheese food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cow milk cheese - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from domesticated bird meat. - Damion Dooley - - poultry meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa. - Damion Dooley - https://en.wikipedia.org/wiki/Suidae - porcine meat - swine food product - - - - - - - - - - - - - - - A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. - Damion Dooley - https://en.wikipedia.org/wiki/Condiment - condiment - condiment food product - - - - - - - - - - - - - - - - - - - - - - - - - - bovine meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - fruit juice food product - - - - - - - - - - - - - - - wheat food product - - - - - - - - - - - - - - - - - - - - - - - - - - A food product deriving primarily from corn (maize). - Damion Dooley - - maize food product - maize (corn) food product - - - - - - - - - A food product derived from or produced by a plant root. - plant root food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A citrus fruit is botanically classified as a type of berry called a hesperidium that has a thick, leathery rind, with numerous oil glands, and a large flesh portion composed of several wedge-shaped sections. Unlike pome fruit, such as the apple, the citrus fruit is derived from a superior ovary, an ovary completely separate from the calyx. - Damion Dooley - https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/hesperidium - citrus - citrus fruit food product - - - - - - - - - - - - - - - - - - citrus fruit juice - - - - - - - - - - - - - - - - - - - - - - - - - - pomes - pomaceous fruit food product - - - - - - - - - - solanaceous fruit food product - - - - - - - - - - - - - - - - A food product deriving from one or more tomatoes. - tomato food product - - - - - - - - - solanaceous food product - - - - - - - - - cruciferous food product - - - - - - - - - - - - - - - - - - - - - - - - - - grape berry food product - - - - - - - - - - - - - - - - - - - - - - - The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling. - Damion Dooley - SUBSET_SIREN:F16972 - nut food product - - - - - - - - - - - - - - - - - - - - - - - - - - plant seed food product - - - - - - - - - - plant lipid food product - - - - - - - - - plant stem food product - - - - - - - - - - - - - - - - - - - - - - - - - - invertebrate animal food product - - - - - - - - - - - - - - - Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. - - prepared - prepared food product - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - cooked - food (cooked) - - - - - - - - - - - - - - - - bread food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - rice food product - - - - - - - - - - wheat flour food product - - - - - - - - - - A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization. - LANGUAL:C0195 - sweet cream - cream food product - - - - - A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization. - http://en.wikipedia.org/wiki/Cream - - - - - - - - - - - - - - - - - - - - - - A sausage made with fresh meats, and then fully cooked. - Damion Dooley - - sausage (cooked) - - - - - - - - - A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche. - creamy salad dressing - - - - - A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche. - http://en.wikipedia.org/wiki/Salad_dressing#Dressings - - - - - - - - - - - - - - - A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier. - mayonnaise food product - - - - - A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier. - http://en.wikipedia.org/wiki/Mayonnaise - - - - - - - - - - - - - - - - - - processed pork meat food product - - - - - - - - - - - - - - - - - A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. - Damion Dooley - http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 - http://www.langual.org/langual_thesaurus.asp?termid=H0151 - herb and spice - herb or spice - spice or herb - - - - - - - - - - animal lipid food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). - Damion Dooley - - fish food product - - - - - - - - - avian food product - - - - - - - - - - plant derived beverage - - - - - - - - - - - - - - - - - - plant derived fermented beverage - - - - - - - - - nonfermented plant derived beverage product - - - - - - - - - - - - - - - - - - - - - - A dairy food product has mammilian milk or a milk component as an ingredient. - Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=H0242 - dairy product - milk product - dairy food product - - - - - - - - - milk or milk based food product - - - - - - - - - - - - - - - - - - Are all fermented foods considered preserved to some extent? - Damion Dooley - food (fermented) - - - - - - - - - - - - - - - - - - - - - Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. - - vegetable food product - - - - - - - - - Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. - botanical fruit food product - - - - - Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. - http://eurovoc.europa.eu/drupal/?q=request&amp;uri=http://eurovoc.europa.eu/1115 - http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119 - http://www.fao.org/pollination/resources/glossary/en/ - https://en.wikipedia.org/wiki/Fruit - - - - - - - - - A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995) - http://www.fao.org/pollination/resources/glossary/en/ - legume - http://purl.obolibrary.org/obo/FOODON_03411338 - http://purl.obolibrary.org/obo/FOODON_03411254 - legume food product - - - - - - - - - - - - - - - A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. - Regarding American regulatory aspects of egg products, see this summary: -https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077 - egg food product - - - - - A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. - Wikipedia:Egg_%28food%29 - - - - - - - - - - - - - - - - - - - - - - - - - - - A hen egg food product is any food product consisting mainly of hen eggs or derivatives. - https://en.wikipedia.org/wiki/Egg_as_food - SUBSET_SIREN:F1074 - hen egg food product - - - - - - - - - - A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. - - - beef mince - beef mince - ground beef - hamburger meat - minced beef - ground beef food product - hamburger meat - - - - - - - - - - - - - - - - A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants. - Damion Dooley - - poultry food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A turkey meat food product is any food product made predominantly of turkey parts. - Damion Dooley - turkey meat food product - - - - - - - - - - - - - - - - A sauce for a salad. - http://en.wikipedia.org/wiki/Salad_dressing#Dressings - salad dressing - - - - - - - - - - - - - - - - - - - - - - - - - - oyster food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - shellfish food product - - - - - - - - - - - - - - - - A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process. - Damion Dooley - food fermentation - - - - - - - - - - - - - - - - - - - - - - - - - - - Fermented meat product is any product made primarily of meat subjected to a fermentation process. - Damion Dooley - fermented meat product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Food trimmings are the parts removed from the culinary trimming of unwanted or inedible parts (i.e. sinews, skin, fat etc.) from meat, fish poultry or vegetables. Trimmings are used for making stocks, soups and sauces. - Gregory Harhay - http://en.foodlexicon.org/p0000380.php - trim - trimmings - food trimming - - - - - - - - - - - - - - - animal product sandwich - - - - - - - - - - - - - - - - - - - - - - - - - - apple condiment - - - - - - - - - - - - - - - - - - - - - - - - - - apple food product - - - - - - - - - - - - - - - - - - - apple vinegar food product - - - - - - - - - - - - - - - - - - - - - - - - - - asparagus vegetable food product - - - - - - - - - - - - - - - - A food product deriving from one or more avocados. - avocado food product - - - - - - - - - - - - - - - bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - berry food product - - - - - - - - - pepper - Pepper - black or white pepper product - pepper - - - - - - - - - - - - - - - black pepper food product - - - - - - - - - - - - - - - - - - carrot juice food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - carrot food product - - - - - - - - - - - - - - - cattle sandwich - - - - - - - - - - - - - - - - - - - - - - - - - - A plant food product derived from a celery plant (Apium graveolens) - - celery food product - - - - - - - - - - - - - - - - - - - - - cheese product analog - - - - - - - - - A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. - food product component - - - - - - - - - - - - - - - A food product deriving from one or more cherries. - cherry food product - - - - - - - - - - condiment sauce - - - - - - - - - - - - - - - - - - - - - - - - - - coriander food product - - - - - - - - - - - - - - - - corn snack - - - - - - - - - - - - - - - - - - - - - - - - - - - - vegetable corn food product - - - - - - - - - - - - - - - - - - - - - - - - - - - cow milk based food product - - - - - - - - - cow milk butter food product - - - - - - - - - - cow milk cream food product - - - - - - - - - - - - - - - cow milk hard cheese food product - - - - - - - - - - - - - - - - - - - - - - - - - - crustacean food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A pickled cucumber (commonly known as a pickle in the United States and Canada or generically as gherkins in the United Kingdom, Ireland, Australia, and New Zealand) is a cucumber that has been pickled in a brine, vinegar, or other solution and left to ferment for a period of time, by either immersing the cucumbers in an acidic solution or through souring by lacto-fermentation. - Damion Dooley - https://en.wikipedia.org/wiki/Pickled_cucumber - cucumber or gherkin pickle food product - - - - - - - - - - - - - - - A food product deriving from one or more cucumbers. - cucumber food product - - - - - - - - - SUBSET_SIREN:F1442 - dairy product analog - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - egg substitute - egg product analog - - - - - - - - - - - - - - - - - - - - - - - - - - fermented cereal beverage - - - - - - - - - - - - - - - - - - - - - field corn based bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A product made from the North American term for maize (Zea mays) grown for livestock fodder (silage), ethanol, cereal and processed food products. The principal field corn varieties are dent corn, flint corn, flour corn (also known as soft corn) which includes blue corn (Zea mays amylacea), and waxy corn. - Damion Dooley - - dry corn food product - dry corn - field corn food product - - - - - - - - - - - - - - - field corn snack food product - - - - - - - - - - - - - - - - - - - - - - - - - - - field corn sweetener product - - - - - - - - - - - - - - - food flavoring or seasoning product - - - - - - - - - food dressing product - - - - - - - - - food product analog - - - - - - - - - - - - - - - - - - - - - - - - - - - garlic food product - - - - - - - - - - - - - - - - - - - - - - - - - - ginger - ginger - ginger food product - - - - - - - - - - - - - - - - - - - - - grain based bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - grain based vinegar food product - - - - - - - - - - - - - - - gravy or sauce - - - - - - - - - - - - - - - - - - - - - - - - - - green bell pepper food product - - - - - - - - - - hot pepper spice food product - - - - - - - - - - - - - - - - - - - - - - - - - - red pepper - hot pepper food product - - - - - - - - - imitation food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product made from a kale plant. - - kale food product - - - - - - - - - - - - - - - - - - - - - - - - - - lemon food product - - - - - - - - - - - - - - - - - - - - - - - - - - lentil vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A lettuce vegetable food product is the head, stem or leaf portion of a lettuce plant. - Damion Dooley - 2019-06-27T13:30:10Z - lettuce - lettuce - lettuce head food product - - - - - - - - - - - - - - - - - macaroni or noodle food product - - - - - - - - - - - - - - - - - - - - - - - - - - milk based gravy or sauce food product - - - - - - - - - - - - - - - - - - - - - - - - - - mollusk food product - mollusc food product - - - - - - - - - nonalcoholic beverage - - - - - - - - - - - - - - - olive fat or oil refined food product - - - - - - - - - - - - - - - - - - - - - onion flavouring food product - - - - - - - - - - - - - - - - - - - - - - - - - - onion food product - - - - - - - - - - - - - - - pancake or waffle food product - - - - - - - - - - - - - - - - - - green or red pepper pickle food product - - - - - - - - - - - - - - - A food product deriving from one or more sweet or hot peppers. - pepper vegetable food product - - - - - - - - - - - - - - - - - - plant based bakery food product - - - - - - - - - - - - - - - - - - - - - plant based refined or partially-refined food product - - - - - - - - - - - - - - - - - An edible plant fat or oil product with characteristics that consumers desire such as bland flavour and odour, clear appearance, light colour, stability to oxidation and suitability for frying, and which is the result of a refining process that removes free fatty acids. - Damion Dooley - plant fat or oil refined food product - - - - - - - - - - - - - - - - A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product. - plant fruit as vegetable food product - - - - - - - - - plant head vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - plant leaf vegetable food product - - - - - - - - - - - - - - - - - - plant product dressing - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product harvested from underground plant parts. - plant root vegetable food product - - - - - - - - - - - - - - - - - - plant seed based bakery food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - plant seed vegetable food product - - - - - - - - - - - - - - - - - - plant stem or spear vegetable food product - - - - - - - - - plant sweetener - - - - - - - - - - Damion Dooley - preserved - food (preserved) - - - - - - - - - - - - - - - - - - - A prepared hen egg product is a product predominantly made of hen egg that has been cooked and may only require defrosting or reheating for consumption. - Damion Dooley - prepared hen egg product - - - - - - - - - - - - - - - - - - - - - - - - - - - red bell pepper food product - - - - - - - - - refined or partially-refined food product - - - - - - - - - - - - - - - salad food product - - - - - - - - - - - - - - - - - - - - - - A sandwich food product is a food product used to create a sandwich. This includes bread as a container, and sandwich ingredients and spreads. - Damion Dooley - sandwich food product - - - - - - - - - - - - - - - - - - - - - - - - - - - sesame food product - - - - - - - - - - - - - - - - - - - - - - - - - - shallot food product - - - - - - - - - - - - - - - - - - - - - - - - - - shrimp food product - - - - - - - - - - - - - - - - Damion Dooley notes: We can't say all soups are cooked there are many chilled soup recipes. - soup food product - - - - - - - - - - - - - - - A food product deriving from one or more squashes. - squash food product - - - - - - - - - stone fruit food product - - - - - - - - - - - - - - - - - - - - - sugar based vinegar food product - - - - - - - - - - - - - - - - - - - - - - - - - - - sugar cane food product - - - - - - - - - sugar maple sweetener food product - - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=H0202 - sweetener food product - - - - - - - - - tomato condiment - - - - - - - - - - - - - - - - - - tomato juice food product - - - - - - - - - - - - - - - - - - - - - - - - - - Curcuma - turmeric food product - - - - - - - - - uncured cheese food product - - - - - - - - - uncured cow milk cheese food product - - - - - - - - - - - - - - - multi-component corn food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - vegetable pickle food product - - - - - - - - - - - - - - - A food product derived from one or more walnuts. - walnut food product - - - - - - - - - - - - - - - - - - - - - - A water food product is a food product derived from H20 (water) in its liquid form. - https://en.wikipedia.org/wiki/Water - SUBSET_SIREN:F10414 - water - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) - Water - water - water food product - - - - - - - - - - - - - - - - - - - - - - - - - - wheat based bakery food product - - - - - - - - - - - - - - - wheat based pastry food product - - - - - - - - - wheat bread food product - - - - - - - - - - - - - - - - - - - - - - - - - - white pepper food product - - - - - - - - - - A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition) - Damion Dooley - food product by meal type - - - - - - - - - food seasoning product - - - - - - - - - - - - - - - A food product consisting of food material derived primarily from a single organism. - Damion Dooley - food product by organism - - - - - - - - - baking supply product - - - - - - - - - - - - - - - - - - - - - - - - - - Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience - - - food - foodstuff - nourishment - sustenance - This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/ - food material - - - - - - - - - - - - - - - - - - - - - - - - - - - A product derived from any variety of mint plant. - Damion Dooley - mint - American Corn Mint, Brook Mint, Canadian Mint, Chinese Mint, Corn Mint, Cornmint Oil, Field Mint Oil, Huile de Menthe, Huile de Menthe des Champs, Japanese Oil of Peppermint, Menta Japonesa, Mentha Arvensis Aetheroleum, Mentha arvensis var. piperascens, Mentha canadensis, Menthe du Canada, Menthe des Champs, Menthe Japonaise, Mint Oil, Minzol, Poleo, Pudina, Putiha. [source: https://www.webmd.com/vitamins-supplements/ingredientmono-616-japanese%20mint.aspx?activeingredientid=616&activeingredientname=japanese%20mint] - mint - mint food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A zucchini food product is a food product deriving from either golden or green zucchini plant cultivars. - Damion Dooley - zucchini food product - - - - - - - - - - - - - - - requires discussion - A process involving the physical transformation of a food source or food product into some derived organic material or food product - Damion Dooley - food transformation process - - - - - - - - - Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] - - Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. - Damion Dooley - https://en.wikipedia.org/wiki/Invertebrate - animal - invertebrate animal - - - - - - - - - - - - - - - - - - Raw apple is apple that has not been subject to cooking or other preservation processes other than by cold storage. - apple (raw) - - - - - - - - - - A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. - Damion Dooley - food product by quality - - - - - - - - - - - - - - - - - - - - - baked - baked food product - food (baked) - - - - - - - - - - - - - - - - - - - - - - - - - - lime fruit food product - - - - - - - - - - A physical object quality which can describe an attribute of a food item or related to a food product. - http://orcid.org/0000-0001-8008-8249 - food object quality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pome fruit of an apple tree (Malus domestica). - http://orcid.org/0000-0002-8844-9165 - apple - A whole apple may include a stem. - Apples - apple (whole) - https://www-atlasobscura-com.cdn.ampproject.org/c/s/www.atlasobscura.com/articles/heritage-appalachian-apples.amp - - - - - - - - - cherry (whole or parts) - - - - - - - - - carrot root (whole or parts) - - - - - - - - - - - - - - - - - - - - - - A food product consisting of food material derived from ingredients sourced from multiple organisms. - Damion Dooley - 2019-01-23T22:40:32Z - multi-ingredient - The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 - -Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? - multi-component food product - - - - - - - - - - Dairy cattle are a type of cattle bred for the ability to produce large quantities of milk, from which dairy products are made. This class covers both male and female members of a dairy breed. - Damion Dooley - https://en.wikipedia.org/wiki/Dairy_cattle - 2019-01-26T22:49:27Z - dairy cattle - https://en.wikipedia.org/wiki/List_of_dairy_cattle_breeds - - - - - - - - - - Taurine cattle (Bos taurus taurus), also called European cattle, are a subspecies of domesticated cattle originating in the Near East. Both taurine cattle and indicine cattle (zebus) are descended from the aurochs. Taurine cattle were originally considered a distinct species, but are now typically grouped with zebus and aurochs into one species, Bos taurus. Most modern breeds of cattle are taurine cattle. - Damion Dooley - https://en.wikipedia.org/wiki/Taurine_cattle - 2019-01-28T02:41:04Z - http://www.langual.org/langual_thesaurus.asp?termid=B5186 - taurine cattle - - - - - - - - - - Pork loin is a cut of meat from a pig, created from the tissue along the dorsal side of the rib cage. - Damion Dooley - https://en.wikipedia.org/wiki/Pork_loin - 2019-04-13T18:58:46Z - pork loin - pork loin - - - - - - - - - - An aquatic invertebrate may live entirely beneath the water, or may live upon its surface or on the plants surrounding it. Some breathe air, others breathe water. To move, they may walk, swim, float, skate, fly or glide on their bellies—or they may not move much at all. - Because snails are members of gastropod, a subclass of molluscs, ... leading to aquatic invertebrates, we can't make aquatic invertebrates disjoint with terrestrial invertebrates. - Damion Dooley - https://nature.mdc.mo.gov/discover-nature/general-species-information/aquatic-invertebrate-facts - 2019-04-29T19:23:38Z - aquatic invertebrate - - - - - - - - - - - - - - - Damion Dooley - 2019-05-21T22:37:06Z - Aves - avian - bird - avian animal - - - - - - - - - - A food product organized by the process which it results from. - Damion Dooley - 2019-05-23T23:02:07Z - food product by process - - - - - - - - - - The largest and main meal of the day, taken either around midday or in the evening. - - Damion Dooley - https://en.wikipedia.org/wiki/Dinner - 2019-05-25T05:03:08Z - dinner - main meal - supper - Main Meal - dinner food - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - 2019-05-25T06:38:12Z - pasteurized - food (pasteurized) - - - - - - - - - Damion Dooley - 2019-06-14T04:23:35Z - pork food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A lipid food product is a food product made primarily of plant or animal fat or oil - Damion Dooley - 2019-06-11T09:18:41Z - fats and oils - oils and fats - lipid food product - - - - - - - - - - A food product made of ground or minced turkey meat - Damion Dooley - 2019-06-28T04:44:34Z - ground turkey - minced turkey - ground turkey - turkey (ground or minced) - - - - - - - - - Damion Dooley - 2019-06-28T00:25:22Z - ginger - ginger root - - - - - - - - - - - - - - - - - A hamburger (short: burger) is a sandwich consisting of one or more cooked patties of ground meat, usually beef, placed inside a sliced bread roll or bun. The patty may be pan fried, grilled, or flame broiled. - Damion Dooley - https://en.wikipedia.org/wiki/Hamburger - 2019-06-28T07:39:11Z - burger - hamburger - Burgers - beef hamburger (dish) - - - - - - - - - - - - - - - - - - - - - - - Food material chopped into roughly bite-sized pieces. - Damion Dooley - 2019-07-09T20:59:57Z - chopped - cut - Cut - food (chopped) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - 2019-07-10T17:35:07Z - SUBSET_SIREN:F4839 - turkey egg - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'egg' (http://purl.obolibrary.org/obo/FOODON_03420194) - turkey egg (whole, shell on, raw) - - - - - - - - - - A whole turkey food product consists of the plucked carcass of a turkey with head and entrails removed and with organ meats and neck severed and possibly included in body cavity. - Damion Dooley - 2019-07-10T19:28:58Z - turkey - turkey - turkey (whole, raw) - https://www.nwtf.org/hunt/article/how-to-clean-wild-turkey - - - - - - - - - - The Granny Smith is a tip-bearing apple cultivar, which originated in Australia in 1868. The tree is thought to be a hybrid of Malus sylvestris, the European wild apple, with the North American apple Malus pumila as the polleniser. - - - 2019-08-07T19:29:34Z - Granny Smith apple tree - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pome fruit of a Granny Smith apple tree cultivar. - - Damion Dooley - - https://en.wikipedia.org/wiki/Granny_Smith - 2019-08-07T19:34:52 - - granny smith apple - Granny Smith apple - Granny Smith apple (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - A hazelnut food product is a food product that derives from hazelnuts - - 2019-08-09T22:59:15Z - hazelnut food product - - - - - - - - - - The hazelnut is the nut of the hazel and therefore includes any of the nuts deriving from species of the genus Corylus, especially the nuts of the species Corylus avellana. It also is known as cobnut or filbert nut according to species. - - Emma Griffiths - - 2019-08-09T23:07:38Z - cobnut - Hazelnuts - hazelnut - - - - - - - - - - - A patty, in American, Canadian, South African, Australian and New Zealand English, is a flattened, usually round, serving of ground food, often meat or meat alternatives. The food is compacted and shaped into the patty, then cooked, and served. - - Emma Griffiths - - 2019-08-11T05:07:26Z - pattie - patties - patty - - - - - - - - - - Gnetum africanum is a vine gymnosperm species found natively throughout tropical Africa. It is grown in various countries across Africa, including: Cameroon. - - Emma Griffiths - - 2019-08-11T22:22:09Z - Gnetum africanum - KoKo - afang - eru - fumbua - m’fumbua - okok - ukase - wild spinach - African jointfir plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of an okazi plant (Gnetum africanum). - - - - https://pfaf.org/user/Plant.aspx?LatinName=Gnetum+africanum - 2019-08-11T22:28:35 - spinach - Gnetum africanum leaf - afang leaf - african jointfir leaf - eru leaf - fumbua leaf - okazi leaf - okok leaf - ukazi leaf - wild spinach leaf - Okazi leaves, often referred to as wild spinach, are used as a leafy vegetable for soups and stews, commonly called eru soup or afang soup, or eaten raw. The leaves may further be used as a remedy for nausea, sore throats, or as a dressing for warts. - okazi leaf (whole) - spinach - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A tuber of an okazi plant (Gnetum africanum). - - - https://pfaf.org/user/Plant.aspx?LatinName=Gnetum+africanum - 2019-08-11T22:31:04 - Gnetum africanum tuber - afang tuber - african jointfir tuber - eru tuber - gnetum africanum tuber - okazi root tuber - ukazi tuber - The okazi root tuber may be used as a source of famine food, and is similar to that of a yam. - okazi tuber - - - - - - - - - - - - - - - - - - - - - - - - - - - The poblano (Capsicum annuum) is a mild chili pepper originating in the state of Puebla, Mexico. Dried, it is called ancho or chile ancho, from the Spanish word ancho ("wide"). - - Emma Griffiths - 2019-08-13T04:55:19Z - ancho - ancho pepper - chile ancho - poblano - ancho pepper - - - - - - - - - - A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. - - - 2019-08-14T18:02:36Z - - animal - - - - - - - - - - A pickled cucumber (commonly known as a pickle in the United States and Canada and a gherkin in Britain, Ireland, Australia, South Africa and New Zealand) is a cucumber that has been pickled in a brine, vinegar, or other solution and left to ferment for a period of time, by either immersing the cucumbers in an acidic solution or through souring by lacto-fermentation. - - - 2019-08-20T19:10:28Z - - gherkin - pickle - Pickles - pickled cucumber - - - - - - - - - - - - - - - - - - - - - - - - - - - A bell pepper is a fruits in different colours - including red, yellow, orange, green, white, and purple - from a bell pepper plant cultivar. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". - - - 2019-08-22T18:01:49Z - - pepper - bell pepper food product - - - - - - - Kham Tran - www.khamtran.com - - - - - - - - - - Golden zucchini is a modern hybrid summer squash (Cucurbita pepo). - - - 2019-08-22T19:52:25Z - gold gush zucchini - golden delight zucchini - goldfinger zucchini - yellow zucchini - golden zucchini plant - - - - - - - - - - - - - - - - - - - - - - - - - - A golden or yellow zucchini is a summer squash harvested from the golden zucchini cultivar. - - 2019-08-22T20:36:52Z - golden zucchini - yellow zucchini - golden zucchini squash (whole) - - - - - - - - - - - - - - - - - - - Sunburst squash is a summer squash (species *Cucurbita pepo*) notable for its small size, round and shallow shape, and scalloped edges, somewhat resembling a small toy top, or flying saucer. - - - 2019-08-22T21:11:29Z - cibleme - pattypan squash - scallopini - sunburst squash - white squash - yellow squash - pattypan squash - pattypan squash (whole, raw) - - - - - - - - - - A shallot is the bulb part of a shallot plant - - 2019-08-22T23:45:59Z - shallot - shallot (whole, raw) - shallots - - - - - - - - - - Damion Dooley - http://langual.org - 2019-08-23T00:37:18Z - SUBSET_SIREN:F11872 - cumin - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - cumin - cumin seed (whole, dried) - - - - - - - - - - 2019-08-24T15:46:35Z - basil - basil - basil food product - - - - - - - - - - A dish made from boiled cornmeal. - - - 2019-08-24T17:49:54Z - corn grits - Grits - grits - - - - - - - - - - - - - - - Malus is a genus of about 30–55 species[3] of small deciduous trees or shrubs in the family Rosaceae, including the domesticated orchard apple (M. pumila syn. M. domestica) – also known as the eating apple, cooking apple, or culinary apple. The other species are commonly known as crabapples, crab apples, crabtrees or wild apples - - 2019-08-25T15:37:56Z - Malus group - - - - - - - - - - A poultry sandwich contains chicken, turkey or other poultry meat. - - Damion Dooley - 2019-08-26T18:45:16Z - poultry sandwich - - - - - - - - - - A variety of kale with a long tradition in Italian cuisine, especially that of Tuscany. - - - 2019-09-11T00:21:19Z - Cavolo nero - Lacinato - Tuscan kale - black Tuscan palm - black cabbage - dinosaur kale - flat back cabbage - palm tree kale - Lacinato kale - lacinato kale - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). - - https://en.wikipedia.org/wiki/Vegetarian_cuisine - 2019-09-11T21:12:43Z - vegetarian food - vegetarian food product - - - - - - - - - - - - - - - - - - - - An adult female chicken. - - 2019-11-15T20:12:48Z - - hen - - - - - - - - - - A food product made from black, white, pink or similar peppercorns. - - 2019-11-15T23:03:24Z - peppercorn food product - - - - - - - - - - 2019-11-15T23:19:38Z - multi-component meat product - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-01-08T00:20:27Z - echinoderm food product - - - - - - - - - A lemon, whole or in pieces, for eating or other food processing. - - 2020-03-28T23:38:10Z - lemon (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A hesperidium fruit of a citrus plant (Citrus). - - https://orcid.org/0000-0001-5275-8866 - 2020-10-20T06:54:39 - citrus fruit - citrus fruit (whole) - - - - - - - - - - - - - - - - - - - - - - A genus of plants in the mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants. - - bok choy vegetable food product - bomdong vegetable food product - broccolini vegetable food product - chinese cabbage vegetable food product - choy sum vegetable food product - collard greens vegetable food product - gai lan vegetable food product - komatsuna vegetable food product - mizuna vegetable food product - rutabaga vegetable food product - savoy cabbage vegetable food product - tatsoi vegetable food product - cole crop vegetable food product - cruciferous vegetable food product - brassica food product - - - - - - - - - - Food contact materials are materials that are intended to be in contact with food. These can be things that are quite obvious like a glass or a can for soft drinks as well as machinery in a food factory or a coffee machine. - - - 2020-07-31T17:07:09Z - food contact material - - - - - - - - - - - - - - - - 2020-09-06T15:59:54Z - multi-component wheat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A seed of a cumin plant (Cuminum cyminum). - - https://en.wikipedia.org/wiki/Cumin - 2020-09-06T16:35:13 - cumin - cumin seed (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A primary root of a carrot plant (Daucus carota). - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T07:27:10 - carrot - carrot - carrot root (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A petiole of a celery plant (Apium graveolens Dulce Group). - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T07:43:45 - celery stalk - celery stalk (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a cucumber plant (Cucumis sativus). - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T14:18:28 - cucumber (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a grape plant. - http://orcid.org/0000-0002-8844-9165 - 2020-09-09T14:38:33 - de-stemmed grape - grape - grape (whole) - - - - - - - - - - - - - - - - 2020-09-09T19:28:43Z - Maize plant - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A stem of an asparagus plant (Asparagus officinalis) - - https://orcid.org/0000-0001-5275-8866 - 2020-10-13T05:48:32 - asaparagus - asparagus spear (whole) - - - - - - - - - A food product which has been separated into pieces. - - 2020-10-12T07:07:16Z - food (pieces) - - - - - - - - - - - - - - - - - - - - - - - - - An edible drupe fruit of a cherry plant. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-13T05:48:32 - cherry - cherries - cherry (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A ripened red colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T12:37:01 - bell pepper - capsicum - pepper - sweet pepper - sweet red bell pepper - Bell pepper - bell pepper - sweet red bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a pepper plant (Capsicum) - - https://orcid.org/0000-0001-5275-8866 - https://www.britannica.com/plant/pepper-plant-Capsicum-genus - 2020-10-14T02:39:11 - pepper - peppers - pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A juicy, rounded, brightly colored fruit without a stone or pit, though pips or seeds may be present. - - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Berry - 2020-10-23T09:28:05 - berry - common berry - berry (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit varietal of a squash plant (Cucurbita). - - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Cucurbita - 2020-10-20T12:01:59 - squash - squash - squash (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit in the Grossum cultivar group of a bell pepper plant. - - 2020-11-19T01:08:58Z - bell pepper - capsicum - pepper - sweet pepper - bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immature green colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T07:08:14 - bell pepper - capsicum - pepper - sweet green pepper - sweet pepper - sweet green bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A mature yellow colored berry fruit of a bell pepper plant cultivar. - - 2020-11-19T01:24:18Z - bell pepper - capsicum - pepper - sweet pepper - sweet yellow pepper - sweet yellow bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of a garlic plant (Allium sativum) - - https://en.wikipedia.org/wiki/Garlic - 2020-11-30T04:49:32 - garlic - garlic - garlic bulb - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immature flower stalk of a garlic plant. - - https://en.wikipedia.org/wiki/Garlic - 2020-12-16T22:45:47 - garlic spear - garlic stem - garlic top - garlic scape - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of an avocado plant (Persea americana) - - https://en.wikipedia.org/wiki/Avocado - 2021-02-10T22:52:57 - avocado - avocado - avocado (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a celery plant (Apium graveolens Dulce Group). - - https://en.wikipedia.org/wiki/Celery - 2021-02-11T02:01:06 - celery leaf - celery leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bunch of a raw celery leaves. - - https://en.wikipedia.org/wiki/Celery - 2021-02-11T02:01:46 - celery bunch - celery bunch - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a grape plant. - - 2021-02-11T02:02:32 - grape leaf - grape leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a vegetable-producing plant. - - 2021-02-11T02:40:22 - vegetable leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - A hesperidium fruit of a lime plant. - - https://en.wikipedia.org/wiki/Lime_(fruit) - 2021-02-11T02:57:03 - lime - lime - lime (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a pattypan squash plant, a varietal of summer squash. - - https://en.wikipedia.org/wiki/Pattypan_squash - 2021-02-11T16:45:15 - button squash - custard squash - pattypan squash - scallop squash - scallopini squash - pattypan squash (whole) - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a summer squash plant. - - https://en.wikipedia.org/wiki/Summer_squash - 2021-02-11T16:47:21 - summer squash - summer squash (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A root of a ginger plant (Zingiber officinale) - - https://en.wikipedia.org/wiki/Ginger - 2021-02-11T17:33:19 - elephant ginger - elephant ginger root - ginger - ginger root - ginger root (whole) - - - - - - - - - - A berry fruit of a chili pepper plant. - - https://en.wikipedia.org/wiki/Chili_pepper - 2021-02-11T21:40:27 - chile pepper - chili - chili pepper - chili pod - chilli - chilli pepper - chile pepper - chili pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of a shallot plant (Allium cepa var. aggregatum) - - https://en.wikipedia.org/wiki/Shallot - 2021-02-11T21:44:21 - shallot - shallot (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A root of a turmeric plant (Curcuma longa) - - https://en.wikipedia.org/wiki/Turmeric - 2021-02-11T22:31:47 - indian saffron - turmeric - yellow ginger - turmeric - turmeric root (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A riped berry fruit of a white pepper plant. - - https://en.wikipedia.org/wiki/Black_pepper - 2021-02-11T23:07:09 - white pepper - white peppercorn - white peppercorn (whole) - - - - - - - - - - An anatomical part of a plant that is consumed by humans or other animals as food. - - https://en.wikipedia.org/wiki/Vegetable - 2021-02-12T18:49:32 - vegetable (whole) - - - - - - - - - - A sausage (usually a hot dog) on a stick that has been coated in a thick layer of cornmeal batter and deep fried. - - https://en.wikipedia.org/wiki/Corn_dog - - 2021-07-19T11:58:23Z - corndog - Corn dogs - corn dog - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pepo fruit of a winter squash plant harvested in the fall. - - https://orcid.org/0000-0002-7463-6306 - https://en.wikipedia.org/wiki/Winter_squash - 2021-07-22T17:39:12 - winter squash - winter squash (whole) - - - - - - - - - - A food product made from feta cheese. - - 2022-01-06T22:23:57Z - feta cheese food product - - - - - - - - - - - A celery food product derived from an Apium graveolens Dulce Group plant. - 2022-01-31T07:44:24Z - celery (Dulce Group) food product - - - - - - - - - A food product deriving from one or more animals. - - 2022-09-01T16:31:09Z - animal food product - - - - - - - - - - A processed material which is referenced in an ingredient specification. - This term could probably go in the COB ontology. - - 2022-08-12T04:23:10Z - ingredient - ingredients - - - - - - - - - - Chickens, turkeys, quail, ducks, and geese are only called poultry if they aren't reared in the wild. - A domesticated bird that is kept by humans for its eggs, meat or feathers. - - 2022-08-25T10:01:00Z - - poultry - - - - - - - - - An unshelled lentil with a brown seed coat and an orange-red cotyledon. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Lentil - 2022-03-28T16:12:32Z - masoor daal - orange lentil - red lentil - pink lentil (whole) - red lentils - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A leaf of a ginger plant (Zingiber officinale). - ginger leaf (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole ginger leaf or some substance made from a processed ginger leaf. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Ginger - 2022-04-13T09:40:25Z - ginger leaf - ginger leaf (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole ginger root or some substance made from a processed ginger root. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Ginger - ginger - ginger root - ginger root (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole tomato or some substance made from a processed tomato. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Tomato - 2022-04-13T12:27:40Z - tomato - tomato - tomato (whole or parts) - tomatoes - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole cucumber or some substance made from a processed cucumber. - https://orcid.org/0000-0001-5275-8866 - cucumber - cucumber (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - Whole kale or some substance made from processed kale. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Kale - 2022-04-13T09:55:24Z - kale - kale - kale (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - A whole black pepper or some substance made from processed black pepper. - https://orcid.org/0000-0001-5275-8866 - black pepper - black pepper - black pepper (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole squash or some substance made from a processed squash. - squash (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1073 - subset_siren - SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - sugar (granulated) - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1115 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'proteolytic fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460102) - - soy sauce - soy sauce - - - - - - - - - - - - - - - - http://langual.org - flour - SUBSET_SIREN:F1116 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - Flour - wheat flour - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1146 - SUBSET_SIREN:F1404 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* immersed in 'packed in salt brine' (http://purl.obolibrary.org/obo/FOODON_03480018) - - cucumber pickle - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1256 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420139) -* has substance added 'flavoring or spice extract or concentrate added' (http://purl.obolibrary.org/obo/FOODON_03460100) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) - - maraschino cherries - maraschino cherry - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1283 - raisin - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present' (http://purl.obolibrary.org/obo/FOODON_03420137) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - raisin (whole) - raisins - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1304 - subset_siren - SIREN DB annotation: -* has quality 'semiliquid' (http://purl.obolibrary.org/obo/FOODON_03430103) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - Batter - batter - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1337 - citrus fruit - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - citrus fruit (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A drupe fruit from a walnut tree (Juglans). - https://en.wikipedia.org/wiki/Walnut - http://langual.org - SUBSET_SIREN:F1364 - walnut - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - walnut (whole) - walnuts - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1440 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460185 - - mayonnaise - mayonnaise - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1441 - lemon - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lemon - lemon (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1444 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - vegetable juice food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a tomato plant (Solanum lycopersicum). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F1453 - tomato - subset_siren - tomato (whole) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1460 - Ketchup - subset_siren - SIREN DB annotation: -* has quality 'semiliquid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430135) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - ketchup - tomato catsup - - - - - - - - - - A concentrated cow milk product is obtained through partial water removal, yeilding milk that has less than the approximate 88% water content that fresh whole milk has. - Damion Dooley - https://www.uoguelph.ca/foodscience/book-page/concentrated-and-dried-dairy-products - http://langual.org - SUBSET_SIREN:F1503 - condensed milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow milk (concentrated) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1505 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'food homogenization or emulsification process' (http://purl.obolibrary.org/obo/FOODON_03460306) -* formed as a result of 'sterilization by heating' (http://purl.obolibrary.org/obo/FOODON_03470123) -* has substance added 'vitamin D' (http://purl.obolibrary.org/obo/CHEBI_27300) -* has substance added 'nutrient or dietary substance added' (http://purl.obolibrary.org/obo/FOODON_03460194) - - evaporated milk - evaporated milk - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1545 - cucumber - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - cucumber (whole, raw) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1570 - carrot - carrot root - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb' (http://purl.obolibrary.org/obo/FOODON_03420238) - - carrot root (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1577 - squash - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - squash (whole, raw) - - - - - - - - - - A rice food product consisting of hulled rice kernels. - http://langual.org - SUBSET_SIREN:F1641 - rice - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - rice - rice kernel food product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1704 - onion - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion - onion (whole, raw) - onions - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1705 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* formed as a result of 'alcohol-acetic acid fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460123) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) -* formed as a result of 'preservation by heat treatment' (http://purl.obolibrary.org/obo/FOODON_03470120) - - vinegar - vinegar - - - - - - - - - - - - - - - - - - - - A whole raw apple is an apple harvested from an apple tree. It may include a stem. It has not been subject to cooking or preservation processes other than cold storage or waxing. - Damion Dooley - http://langual.org - SUBSET_SIREN:F1710 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - apple (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1727 - celery - celery stalk - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'stem or stalk (without leaves)' (http://purl.obolibrary.org/obo/FOODON_03420101) - - celery - celery stalk (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1774 - subset_siren - asparagus (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1826 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - olive oil - olive oil - https://static.oliveoiltimes.com/library/ioc-olive-oil-standard.pdf - - - - - - - - - - - - - - - - A spice mixture that is made from finely ground spices and is used for making curry. - http://langual.org - SUBSET_SIREN:F1842 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - curry powder - curry powder - - - - - - - - - - - A seasoning made from dried garlic flake that has been ground into a powder. - http://langual.org - - SUBSET_SIREN:F1844 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'root, tuber or bulb, without peel' (http://purl.obolibrary.org/obo/FOODON_03420240) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - garlic powder - garlic powder - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1848 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) - - maple syrup - maple syrup - - - - - - - - - - - - - - - - - - - - http://langual.org - 2019-08-26T14:29:56Z - SUBSET_SIREN:F1886 - SUBSET_SIREN:F5599 - raw beef hamburger - subset_siren - SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) - - ground beef (raw) - - - - - - - - - - A sandwich is a food typically consisting of vegetables, sliced cheese or meat, placed on or between slices of bread, or more generally any dish wherein two or more pieces of bread serve as a container or wrapper for another food type. - - http://langual.org - SUBSET_SIREN:F1906 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 1.5-7 cm.' (http://purl.obolibrary.org/obo/FOODON_03430105) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* formed as a result of 'food filling process' (http://purl.obolibrary.org/obo/FOODON_03460207) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - sandwich - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1924 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420139) -* formed as a result of 'food baking process' (http://purl.obolibrary.org/obo/FOODON_03450005) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added 'sucrose added' (http://purl.obolibrary.org/obo/FOODON_03460158) - - apple (baked) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1940 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) - - baking powder - baking powder - - - - - - - - - - - - - - - - A liquid prepared for consumption, or a product that can be combined with water or milk to make one. - Damion Dooley - http://langual.org - 2019-09-12T00:00:00 - beverage food product - - - - - - - - - - - - - - - - - - - - - - Fruit which has not been subjected to heat treatment, but which may have other mechanical processes such as slicing applied to it. - http://langual.org - SUBSET_SIREN:F2007 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit (raw) - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2008 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - vegetable (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2030 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'pod or seed' (http://purl.obolibrary.org/obo/FOODON_03420158) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - chili powder - chili powder - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2052 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* has substance added 'fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460221) - - corn chip - corn chips - - - - - - - - - - - http://langual.org - milk - SUBSET_SIREN:F2116 - cow milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - cow milk (liquid) - milk - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2386 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lemon beverage - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2458 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) -* formed as a result of 'interior bacteria curing process' (http://purl.obolibrary.org/obo/FOODON_03460328) - - Cheddar cheese - cheddar cheese - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2515 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'cream food product' (http://purl.obolibrary.org/obo/FOODON_00001216) -* formed as a result of 'lactic acid fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460101) -* formed as a result of 'food homogenization or emulsification process' (http://purl.obolibrary.org/obo/FOODON_03460306) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - sour cream - sour cream - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2653 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - cooking oil - cooking oil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2676 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* has substance added 'flavoring or taste ingredient added' (http://purl.obolibrary.org/obo/FOODON_03460117) - - imitation maple sweetener - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2695 - subset_siren - SIREN DB annotation: -* has quality 'sliced, thick, between 0.5 and 1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430124) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'griddle cooking' (http://purl.obolibrary.org/obo/FOODON_03450008) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460184 -* has substance added http://purl.obolibrary.org/obo/FOODON_03460186 -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - French Toast - french toast - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2726 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity' (http://purl.obolibrary.org/obo/FOODON_03430102) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - chili seed oil - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2735 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - pork (raw) - - - - - - - - - - - - - - - - A seed, fruit, root, bark, or other plant substance that is primarily used for flavouring or colouring food. - https://en.wikipedia.org/wiki/Spice - http://langual.org - SUBSET_SIREN:F3380 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - spice - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4007 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430121) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) -* has substance added 'animal fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460262) - - enchilada sauce - enchilada sauce - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4152 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - sesame oil - sesame oil - - - - - - - - - - A spice product which is a mixture of more than one spice. - https://en.wikipedia.org/wiki/Spice_mix - http://langual.org - https://orcid.org/0000-0001-8008-8249 - https://orcid.org/0000-0002-8844-9165 - https://orcid.org/0000-0002-9578-0788 - SUBSET_SIREN:F4292 - spice blend - spice mix - subset_siren - Spice mixes can be whole or in parts, but are most commonly blended spices or herbs. - -SIREN DB annotation: -* has quality 'whole and pieces' (http://purl.obolibrary.org/obo/FOODON_03430104) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - spice mixture (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4497 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - edible seed food product - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4583 - subset_siren - SIREN DB annotation: -* has quality 'semiliquid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430135) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) - - chili sauce - chili sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4616 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'shelled egg' (http://purl.obolibrary.org/obo/UBERON_0007379) - - hen egg (whole, shell on, raw) - - - - - - - - - - - - - - - - - - - Note that this allows for several kinds of fruit in one sample, e.g. "some fruit (whole,raw)" allows "apple (whole, raw)" and "orange (whole, raw)". - Damion Dooley - http://langual.org - SUBSET_SIREN:F4644 - fruit - fruits - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - Fruit - fruit (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F4706 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271) -* has substance added 'flavoring or taste ingredient added' (http://purl.obolibrary.org/obo/FOODON_03460117) - - imitation maple syrup - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product derived from one or more turkey eggs. - Damion Dooley - http://langual.org - turkey egg food product - - - - - - - - - - - - - - - - http://langual.org - egg white - SUBSET_SIREN:F4840 - egg albumen food product - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity' (http://purl.obolibrary.org/obo/FOODON_03430102) -* derives from 'albumen' (http://purl.obolibrary.org/obo/UBERON_0008944) - - egg whites - hen egg white food product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5086 - lime - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lime (whole, raw) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5146 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 1.5-7 cm.' (http://purl.obolibrary.org/obo/FOODON_03430105) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'color added' (http://purl.obolibrary.org/obo/FOODON_03460150) -* immersed in 'packed in heavily sweetened liquid' (http://purl.obolibrary.org/obo/FOODON_03480012) - - imitation maraschino cherry - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5263 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - vegetable oil - vegetable oil - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5364 - subset_siren - SIREN DB annotation: -* formed as a result of 'sterilization by irradiation' (http://purl.obolibrary.org/obo/FOODON_03470113) - - food (irradiated) - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5428 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - Lemon juice - lemon juice - lemon juice - - - - - - - - - - An hors d'oeuvre (French: hors-d'œuvre), appetizer or starter is a small dish served before a meal in European cuisine. Typically smaller than a main dish, an hors d'oeuvre is often designed to be eaten by hand. - Damion Dooley - https://en.wikipedia.org/wiki/Hors_d%27oeuvre - http://langual.org - SUBSET_SIREN:F5516 - appetizer - canapé - subset_siren - Appetizer - Appetizers - hors d'oeuvre - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F5609 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow milk (pasteurized) - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6160 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lime juice - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6255 - subset_siren - SIREN DB annotation: -* has quality 'sliced, thick, between 0.5 and 1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430124) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'food toasting process' (http://purl.obolibrary.org/obo/FOODON_03450010) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) - - toast - toast - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6347 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - Pasta - pasta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - http://langual.org - 2019-06-15T02:12:40Z - SUBSET_SIREN:F16329 - SUBSET_SIREN:F6409 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* formed as a result of 'food homogenization or emulsification process' (http://purl.obolibrary.org/obo/FOODON_03460306) - mayonnaise analog - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6429 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - meat (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6581 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow whole milk (pasteurized) - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6667 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* derives from 'fructose' (http://purl.obolibrary.org/obo/CHEBI_28757) -* has substance added 'nonnutritive sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460108) -* has substance added 'flavoring or taste ingredient added' (http://purl.obolibrary.org/obo/FOODON_03460117) -* has consumer 'energy special claim or use' (http://purl.obolibrary.org/obo/FOODON_03510045) - - imitation maple syrup (artificially sweetened) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6726 - green bell pepper - green pepper - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* has quality 'unripe or immature' (http://purl.obolibrary.org/obo/FOODON_03530051) -* derives from 'pod containing small, immature seed' (http://purl.obolibrary.org/obo/FOODON_03420169) - - green bell pepper - sweet green pepper (whole, raw) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6944 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460186 - - Noodles - noodle - noodles - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6952 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - imitation noodle - - - - - - - - - - - A Greek brined curd white cheese made from sheep's milk or from a mixture of sheep and goat's milk. - - http://langual.org - SUBSET_SIREN:F7280 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245) -* formed as a result of 'lactic acid-other agent fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460107) - - feta cheese - feta cheese - - - - - - - - - - http://langual.org - SUBSET_SIREN:F7345 - subset_siren - SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157) - - sugar (refined) - - - - - - - - - - - - - - - - - - - - - - http://langual.org - raw milk - SUBSET_SIREN:F7455 - milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* has consumer 'not pasteurized claim or use' (http://purl.obolibrary.org/obo/FOODON_03510121) - - cow milk (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F7555 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* has substance added 'nonnutritive sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460108) -* has consumer 'dietary claim or use' (http://purl.obolibrary.org/obo/FOODON_03510023) - - imitation sugar - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9389 - subset_siren - Note - curators are implementing "whole or pieces" rather than "whole and pieces". -SIREN DB annotation: -* has quality 'whole and pieces' (http://purl.obolibrary.org/obo/FOODON_03430104) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb' (http://purl.obolibrary.org/obo/FOODON_03420238) - carrot root (raw, whole or parts) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9462 - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'broth or stock' (http://purl.obolibrary.org/obo/FOODON_03420170) - - broth - broth - - - - - - - - - - - - - - - - - - - A meat part that has been cut from a large piece of meat and is too small to be sold individually. - https://www.merriam-webster.com/dictionary/meat%20scrap - http://langual.org - - SUBSET_SIREN:F9475 - meat scrap - meat trim - meat trim - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) -* formed as a result of 'cooking with inherent fat or oil' (http://purl.obolibrary.org/obo/FOODON_03450030) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'partial fat removal process' (http://purl.obolibrary.org/obo/FOODON_03460247) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) -* has consumer 'animal as consumer' (http://purl.obolibrary.org/obo/FOODON_03510021) - - meat trimming - - - - - - - - - - - - - - - - - - - definition: Shrimp paste or shrimp sauce is a fermented condiment commonly used in Southeast Asian, Northeastern South Asian and Southern Chinese cuisines. - Need to set languages of synonyms (japanese/thai ?) - http://orcid.org/0000-0002-1816-4260 - - http://langual.org - SUBSET_SIREN:F9823 - shrimp sauce - bagoong alamang - bagoong aramang - belacan - belachan - blachang - hae ko - hom ha - kapi - mắm ruốc - mắm tép - mắm tôm - ngapi - sidol - terasi - subset_siren - SIREN DB annotation: -* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'whole animal or most parts used' (http://purl.obolibrary.org/obo/FOODON_03420173) -* formed as a result of 'fermentation/modification process, multiple component' (http://purl.obolibrary.org/obo/FOODON_03460128) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* formed as a result of 'preservation by fermentation' (http://purl.obolibrary.org/obo/FOODON_03470104) - - shrimp paste - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9840 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - ginger root (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10351 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'butter' (http://purl.obolibrary.org/obo/FOODON_00001023) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - butter - butter - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10387 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - oil - oil - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10490 - ground ginger - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb' (http://purl.obolibrary.org/obo/FOODON_03420238) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - ginger (ground) - ground ginger - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10573 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 1.5-7 cm.' (http://purl.obolibrary.org/obo/FOODON_03430105) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* has quality 'meat color, undesignated or unknown (deprecated)' (http://purl.obolibrary.org/obo/FOODON_03530003) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) -* formed as a result of 'food baking process' (http://purl.obolibrary.org/obo/FOODON_03450005) -* formed as a result of 'food filling process' (http://purl.obolibrary.org/obo/FOODON_03460207) -* formed as a result of 'carbohydrate fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460256) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - turkey sandwich - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A seed of a lentil plant (Lens culinaris). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F10641 - lentil - subset_siren - lentil (whole) - lentils - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A seed of a legume plant in the family Fabaceae. - https://orcid.org/0000-0001-5275-8866 - http://langual.org - 2020-10-21T09:28:28 - SUBSET_SIREN:F10646 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - legume (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10710 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness <0.3 cm.' (http://purl.obolibrary.org/obo/FOODON_03430153) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* formed as a result of 'food alkalization process' (http://purl.obolibrary.org/obo/FOODON_03460206) -* has substance added 'vegetable fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460263) - - Tortilla chips - tortilla chip - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10780 - cow whole milk - whole milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - cow whole milk 3.5% fat - whole milk - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10784 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) - - fermented vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole apple or some substance made from processed apple. - Damion Dooley - http://langual.org - SUBSET_SIREN:F10788 - apple - subset_siren - apple (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damion Dooley - http://langual.org - zucchini - SUBSET_SIREN:F10943 - green zucchini - zucchini squash - courgettes - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - zucchini - zucchini squash (whole) - - - - - - - - - - A food product that has not been cooked. - http://langual.org - SUBSET_SIREN:F11126 - subset_siren - SIREN DB annotation: -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) - - food (raw) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11146 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - Sauces - sauce - sauce - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11349 - asparagus - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'spear or shoot' (http://purl.obolibrary.org/obo/FOODON_03420186) - - asparagus - asparagus spear (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11353 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'leaf' (http://purl.obolibrary.org/obo/FOODON_03420200) - - carrot top (raw) - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11507 - subset_siren - SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - pork trimming - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11552 - subset_siren - SIREN DB annotation: -* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) - - dough - dough - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11737 - subset_siren - processed food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A cumin food product is derived from the seed of a cumin plant. - Damion Dooley - http://langual.org - cumin - cumin food product - - - - - - - - - - - - - - - - snack - A snack is a small portion of food and generally eaten between meals. - Damion Dooley - - http://langual.org - SUBSET_SIREN:F15013 - subset_siren - snack food - - - - - - - - - - Hen egg substance is food material derived from a hen egg - http://langual.org - SUBSET_SIREN:F15102 - subset_siren - SIREN DB annotation: -* derives from 'egg' (http://purl.obolibrary.org/obo/FOODON_03420194) - - hen egg substance - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A hesperidium fruit of a lemon plant (Citrus limon) - http://langual.org - SUBSET_SIREN:F15104 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - lemon (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15150 - subset_siren - SIREN DB annotation: -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - mammalian milk product - - - - - - - - - - A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish. - Damion Dooley - http://langual.org - SUBSET_SIREN:F15173 - subset_siren - SIREN DB annotation: -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - fish product (unspecified species) - https://en.wikipedia.org/wiki/Fish_products - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15259 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 0.3-1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430140) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* formed as a result of 'griddle cooking' (http://purl.obolibrary.org/obo/FOODON_03450008) - - waffle - waffle - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15272 - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) -* has substance added 'sucrose added' (http://purl.obolibrary.org/obo/FOODON_03460158) - - pastry - pastry - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole vegetable or some substance made from a processed vegetable. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Vegetable - 2022-04-13T09:20:12Z - vegetable - Vegetable - Vegetables - vegetable - vegetable (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15552 - juice - subset_siren - juice beverage - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15614 - subset_siren - SIREN DB annotation: -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - berry product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15615 - subset_siren - SIREN DB annotation: -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit food product - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15708 - subset_siren - Condiments - condiment - - - - - - - - - - - - - - - - http://langual.org - yolk - SUBSET_SIREN:F15772 - subset_siren - SIREN DB annotation: -* derives from 'egg yolk' (http://purl.obolibrary.org/obo/UBERON_0007378) - - hen egg yolk food product - yolks - - - - - - - - - - The chili pepper is the fruit of plants from the genus Capsicum which are members of the nightshade family, Solanaceae. - Damion Dooley - https://en.wikipedia.org/wiki/Chili_pepper - http://langual.org - SUBSET_SIREN:F15873 - chile - chile pepper - chilli - chilli pepper - chīlli - green chili - green chilli pepper - red chili pepper - chili pod - green chilies - subset_siren - The color of the chili can vary depending on its harvest time. - -SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - chili pepper - - - - - - - - - - Is this red bell pepper entry different from "Sweet red bell pepper"? - http://langual.org - SUBSET_SIREN:F15874 - red bell pepper - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming, thickness 0.3-1.5 cm.' (http://purl.obolibrary.org/obo/FOODON_03430140) -* derives from 'pod or seed' (http://purl.obolibrary.org/obo/FOODON_03420158) - - red bell pepper (whole, raw) - red bell peppers - - - - - - - - - - - - - - - A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder. - https://en.wikipedia.org/wiki/Sausage - http://langual.org - - SUBSET_SIREN:F15904 - sausage - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - sausage (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16042 - subset_siren - Salad - salad - - - - - - - - - - An egg produced by a chicken hen. - http://langual.org - egg - SUBSET_SIREN:F16061 - chicken egg - hen egg - subset_siren - This term is ambiguous about whether shell remains on egg or not, i.e. this encompasses both an uncooked egg in shell, or a boiled peeled egg, or a fried egg. - -SIREN DB annotation: -* derives from 'whole egg' (http://purl.obolibrary.org/obo/FOODON_03420274) - Eggs - eggs - hen egg (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16133 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420139) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'color added' (http://purl.obolibrary.org/obo/FOODON_03460150) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - cocktail cherry - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16271 - subset_siren - SIREN DB annotation: -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) - - sugar product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of an onion plant (Allium cepa). - https://orcid.org/0000-0001-5275-8866 - http://langual.org - 2020-10-21T05:43:41 - SUBSET_SIREN:F16347 - bulb onion - common onion - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion (whole) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16449 - subset_siren - SIREN DB annotation: - - dough raising agent - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16453 - subset_siren - seasoning substance - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole or processed walnut. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Walnut - http://langual.org - - 2022-04-13T12:47:02Z - SUBSET_SIREN:F16466 - walnut - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - walnut (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16490 - subset_siren - SIREN DB annotation: -* has quality 'finely ground' (http://purl.obolibrary.org/obo/FOODON_03430106) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - - seasoning, powdered - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16563 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) -* has substance added 'sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460202) - - gherkin pickle - http://www.differencebetween.net/object/comparisons-of-food-items/difference-between-gherkins-and-pickles/ - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16579 - subset_siren - SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - multi-component plant food product - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16694 - subset_siren - SIREN DB annotation: -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - - vegetable fat food product - - - - - - - - - - A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). - http://langual.org - SUBSET_SIREN:F17170 - subset_siren - SIREN DB annotation: -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - meat (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F17238 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - spice (capsicum-based) - - - - - - - - - - http://langual.org - chili - chilli - SUBSET_SIREN:F17304 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with solid pieces' (http://purl.obolibrary.org/obo/FOODON_03430134) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460191 -* has substance added http://purl.obolibrary.org/obo/FOODON_03460212 - - chili con carne with beans (dish, vegetarian) - chilis - - - - - - - - - - - http://langual.org - 2019-08-26T14:16:46Z - SUBSET_SIREN:F10762 - SUBSET_SIREN:F17336 - SUBSET_SIREN:F17337 - beef hamburger patty - beef patty - beefburger - subset_siren - SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) - - ground beef patty - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F17492 - subset_siren - cheese analog, dairy-based - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F17654 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'whole animal or most parts used' (http://purl.obolibrary.org/obo/FOODON_03420173) -* has substance added 'spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460151) -* has substance added 'grain added' (http://purl.obolibrary.org/obo/FOODON_03460152) -* has substance added http://purl.obolibrary.org/obo/FOODON_03460184 - - oyster sauce - oyster sauce - - - - - - - - - - Milk modified by adding acid-producing and/or flavor-producing bacteria under controlled conditions. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0101 - milk product, cultured - cultured milk product (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0102 - crepe, dinner - taco, prepared - prepared food product with bakery base or enclosure, unsweetened (us cfr) - - - - - - - - - - Liquid food prepared from fruit (21 CFR 146). Products prepared from fruit juice by thickening with pectin are indexed under *FRUIT JELLY*; those thickened with gelatin are under *FRUIT BUTTER, JELLY, PRESERVE OR RELATED PRODUCT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0104 - fruit juice or related product (us cfr) - - - - - - - - - - Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0105 - condiment, dressing, gravy or sauce - gravy, condiment, dressing or sauce - sauce, condiment, dressing or gravy - dressing, condiment, gravy or sauce (us cfr) - - - - - - - - - - Food product prepared by drying and/or cooking a mixture of milled grain or non-grain starch with a liquid and usually other ingredients such as sweeteners or fats. Includes sweetened and unsweetened bakery products, macaroni or noodle products and breakfast cereals. Excludes *PUDDING, STARCH*, which is under *CUSTARD OR PUDDING*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0106 - prepared grain or starch product (us cfr) - - - - - - - - - - Includes breads, crackers, pie or pizza crusts and pretzels. Excludes glazed, filled or frosted bakery products, which fall under *BAKERY PRODUCT, SWEETENED* and unsweetened filled products that fall under *PREPARED FOOD PRODUCT WITH BAKERY BASE OR ENCLOSURE, UNSWEETENED* or the appropriate narrower term. See 21 CFR for description of some subgroups. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0107 - crepe, unfilled - unfilled crepe - unsweetened bakery product - bakery product, unsweetened (us cfr) - - - - - - - - - - - - - - - - Beverage containing no more than 0.5% alcohol; it may be flavored, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices, diluted fruit juices and vegetable juices. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0112 - malt beverage, nonalcoholic - nonalcoholic beverage (us cfr) - - - - - - - - - - Aromatic or pungent plant product used whole or ground as a seasoning in food products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0113 - herb or spice - spice or herb (us cfr) - - - - - - - - - - Natural cheese, cured or uncured, cheese product (which is further processed), or cheese product analog. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0115 - cheese or cheese product (us cfr) - - - - - - - - - - - A substance having greater than 2% of the caloric value of sucrose per equivalent unit of sweetening capacity. For example, the amount of such subtance having the sweetening capacity of 1 teaspoon of sucrose would have more than 0.4 calories (21 CFR 170.3(o)(21)). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0118 - nutritive carbohydrate sweetener - sweetener, nutritive - nutritive sweetener (us cfr) - - - - - - - - - - Any form of whole or milled grain, prepared grain product or starch containing product derived from non-grain sources. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0125 - grain or starch product (us cfr) - - - - - - - - - - The liquid extracted or expressed from mature fruit with or without the application of heat. Includes concentrated juice and single-strength juice. If the single-strength juice is prepared from concentrate, then *WATER ADDED* should be used. Carbonated fruit juices are indexed by *FRUIT JUICE* or *FRUIT JUICE, DILUTED* and *CARBONATED* or the appropriate narrower term. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0127 - juice, fruit - fruit juice (us cfr) - - - - - - - - - - Food product having functional characteristics similar to those of cheese or cheese product; it may be nutritionally equivalent or inferior to the product it purports to resemble. The ingredients may or may not be milk-based. An example is a cheese-like product made from skim milk and vegetable oil. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0128 - cheese substitute - cheese, imitation - imitation cheese - cheese product analog (us cfr) - - - - - - - - - - Extract, concentrate or isolate derived from a food source through one or more refining steps (see *EXTRACT, CONCENTRATE OR ISOLATE OF PLANT OR ANIMAL*) and marketed as such. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0129 - refined or partially-refined food product (us cfr) - - - - - - - - - - Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0133 - seasoning or flavoring - flavoring or seasoning (us cfr) - - - - - - - - - - Includes cakes, cookies, pies, quick breads, doughnuts and related products, also bakery products that are glazed, frosted or have a sweetened filling. If sugar is not the first ingredient, *SUGAR OR SUGAR SYRUP ADDED* as well as *SWEETENER ADDED* (or the appropriate narrower term under each) should be indexed in *H. TREATMENT APPLIED*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0135 - crepe, dessert - dessert crepe - sweetened bakery product - bakery product, sweetened (us cfr) - - - - - - - - - - Dressing for which no standards of identity are specified in the CFR. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0136 - nonstandardized dressing (us cfr) - - - - - - - - - - A multiple-component food product typically containing a protein source, a vegetable, and a potato, rice or cereal-based component packaged to be served after heating, either as separate items or courses or mixed as recipe components; see 21 CFR 102.26, 102.28 and 104.47 for nutritional quality guidelines. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0139 - compartmentalized dinner - dinner with components separated in serving containers - dinner, compartmentalized - food packs with separate components - heat and serve dinner - multiple-course dinner - tv dinner - multicomponent meal (us cfr) - - - - - - - - - - Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0143 - pie filling, fruit - fruit or fruit product (us cfr) - - - - - - - - - - Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0148 - milk or milk product (us cfr) - - - - - - - - - - Food product prepared by milling a grain or by producing flour, meal or grits from a non-grain source such as beans, starchy roots or tubers. Refined starch is indexed under *REFINED OR PARTIALLY REFINED FOOD PRODUCT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0149 - milled grain or starch product (us cfr) - - - - - - - - - - Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0150 - meat or meat product (from mammal) (us cfr) - - - - - - - - - - Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0152 - vegetable or vegetable product (us cfr) - - - - - - - - - - Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0164 - dairy product (us cfr) - - - - - - - - - - Natural cheese that is cured; includes cheeses that are normally consumed cured but may be sold in an uncured or very lightly cured stage. The classification of cured cheeses is based on the method of curing, the moisture content, and the milk fat content measured as the proportion of solids. Scope notes given for the general classes give moisture and milkfat proportions that cover the entire range specified in the CFR for the individual cheeses included in a class; the class definition given in the CFR section cited may be more restrictive. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0168 - cheese, cured - cured cheese (us cfr) - - - - - - - - - - Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0172 - prepared dish - prepared food product (us cfr) - - - - - - - - - - Unsweetened bakery product that may be unleavened or yeast-leavened and may be baked in various forms. Excludes pie crust. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0178 - bun, roll, or bread - roll, bun, or bread - bread (us cfr) - - - - - - - - - - Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0179 - relish or condiment - condiment or relish (us cfr) - - - - - - - - - - Substance that is added to food or that is used to treat food and that becomes a component of the food or otherwise affects the functional or nutritional characteristics of the food; for purposes of this vocabulary it excludes products that fall under other categories, such as flavors and sweeteners. - Damion Dooley - FDA CFSAN 1995 - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0181 - food additive (us cfr) - - - - - - - - - - - - Natural cheese that is not cured or is cured for less than 7 days. It may undergo some further processing, such as creaming. It is consumed fresh and has a mild acid flavor. Moisture max. 80%. Includes such products as cottage cheese, cream cheese and mozzarella cheese. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0185 - soft cheese - uncured cheese (us cfr) - - - - - - - - - - Cured cheese ripened by bacteria. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0186 - LanguaL curation note: Used for cheeses, which contain not more than 39 percent of moisture, and their solids contain not less than 50 percent of milkfat [21 CFR Ch. I (4-1-99 Edition)] - hard cheese (us cfr) - - - - - - - - - - Cheese made from milk or milk components, such as cream, by the following process: (1) produce curd through coagulation of milk by bacterial action and/or enzymes and/or acidification and draining of whey. (2) For cured cheese only: cure the curd. Excludes products made through further processing, such as comminuting (see *CHEESE PRODUCT*). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0187 - natural cheese (us cfr) - - - - - - - - - - Prepared grain product made by baking or frying. Includes doughs, batters and mixes. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0191 - bakery product (us cfr) - - - - - - - - - - A thin, sweetened bakery product griddled or cooked in a heated mold. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0194 - waffle or pancake - pancake or waffle (us cfr) - - - - - - - - - - A liquid food made by simmering meat, poultry, seafood or vegetables, being clear or thickened to the consistency of a thin puree or having milk or cream added, and often containing pieces of solid food such as meat, shellfish, pasta or vegetables. Soup takes precedence over other food products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0198 - soup (us cfr) - - - - - - - - - - Sweetened bakery product consisting of a sweetened or unsweetened pastry shell or enclosure containing a sweetened filling, usually fruit, cheese or custard. Examples would be apple strudel, danish pastry or cream puff. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0202 - pastry, sweetened (us cfr) - - - - - - - - - - A combination of one or more vegetable, fruit, herb, meat, poultry, seafood, egg, cereal or pasta, usually served with some kind of moist dressing; may be molded with a jelling agent. Salad takes precedence over other product types. Examples are egg salad, tuna salad, mixed vegetable salad, jelled fruit salad and macaroni salad. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0208 - salad (us cfr) - - - - - - - - - - Natural or synthetic product, dissolved in a suitable solvent or carried on an appropriate dry base and added to a food product to enhance or impart taste and aroma. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0215 - aroma - flavoring (us cfr) - - - - - - - - - - Products of the flesh of animals. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0217 - meat, poultry, seafood or related product (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0218 - LanguaL curation note: Sandwich takes precedent over other product types. Examples: peanut butter and jelly sandwich, tuna sandwich, egg salad sandwich or hamburger on roll. The filling of a sandwich is always indexed as the food source, even if the bread is the same weight or outweighs the filling ingredient(s). The bread would be indexed by *GRAIN ADDED* or the appropriate narrower term. - sandwich (us cfr) - - - - - - - - - - This category includes a wide variety of products made from comminuted or chopped meat (skeletal and/or organ meat) that is usually salted and/or seasoned and often stuffed in an edible or inedible casing. Includes products such as pork sausage, pickle or pimiento loaf, meat spread and pate, and products made by binding meat chunks with gelatin or other binders, such as sectioned and formed ham, beef rolls, and headcheese. Excludes plain ground meat, meat loaf and products made by slicing intact muscle or other tissue, even if packaged and marketed like luncheon meat. Index all processes applied to the product at hand; examples: *FULLY HEAT TREATED*, *CURED FOR 2 MONTHS*, *SMOKED*, *FERMENTED*, *EMULSIFIED OR HOMOGENIZED*. Also consider *PARTICLE SIZE IN SOLID FORMED PRODUCTS* and *TYPEOF SAUSAGE CASING* in *Z. ADJUNCT CHARACTERISTICS OF FOOD*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0221 - luncheon meat - sausage or luncheon meat (us cfr) - - - - - - - - - - Unsweetened food product marketed for consumption between meals; excludes nuts, edible seeds, and sweetened products such as cakes, puddings and candies. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0228 - snack food (us cfr) - - - - - - - - - - - - - - - - - - - - - - - - Alcoholic or nonalcoholic beverage; excludes milk and milk-based beverages, fruit juices and fruit juice drinks, and vegetable juices. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0229 - beverage (us cfr) - - - - - - - - - - A product added to a food item to achieve some degree of sweet taste; it may be nutritive or nonnutritive. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0237 - sweetener (us cfr) - - - - - - - - - - A soup in which the liquid phase has low viscosity. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0243 - bouillon - consomme - soup, thin (us cfr) - - - - - - - - - - Fruits and vegetables in all forms. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0257 - fruit or vegetable product (us cfr) - - - - - - - - - - Nuts in all forms, including nut butters and pastes. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0260 - nut or nut product (us cfr) - - - - - - - - - - Fresh egg in shell, liquid, frozen, dried egg or egg component, or egg product analog. Includes boiled, poached, scrambled, and fried eggs. Excludes prepared egg dishes, such as omelettes. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0261 - egg or egg product (us cfr) - - - - - - - - - - Pourable condiment that is usually applied after the food is prepared but can also be used in cooking. Examples are soy sauce, pepper sauce or barbeque sauce. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0263 - sauce, condiment - condiment sauce (us cfr) - - - - - - - - - - The liquid extracted or expressed from mature vegetables with or without optional ingredients such as seasoning or salt. Products prepared from vegetable juice by thickening with gelatin or pectin are indexed under the broader term *VEGETABLE OR VEGETABLE PRODUCT*. For part or portion, index the part or the plant from which the juice was extracted, rather than *PLANT EXTRACT, CONCENTRATE, OR ISOLATE*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0264 - juice, vegetable - vegetable juice (us cfr) - - - - - - - - - - Flesh from fish or shellfish. Includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0267 - seafood or seafood product (us cfr) - - - - - - - - - - Vegetable product prepared by immersing vegetable in a brine or an acid solution. Often this treatment induces fermentation and/or other changes in the product. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0271 - pickle, vegetable - vegetable pickle (us cfr) - - - - - - - - - - Meat (flesh and organs including blood and bone marrow) from poultry. Used for poultry meat in all forms including poultry product analogs and poultry-based sausage or luncheon meat. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0273 - poultry or poultry product (us cfr) - - - - - - - - - - A prepared grain or starch product made by forming units of dough composed of one or more flours, water and other ingredients. Macaroni, spaghetti and vermicelli may have *EGG WHITE ADDED*, but not egg yolk. Noodles, egg macaroni, egg spaghetti and egg vermicelli have *EGG YOLK ADDED* and should be so indexed. This refers to macaroni or noodles used as ingredients; excludes *PASTA DISH*, which is found under *PREPARED FOOD PRODUCT* (21 CFR 139). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0275 - macaroni or noodle product (us cfr) - - - - - - - - - - Standardized or nonstandardized mixture of edible fats or oils, acidifying agents and optional ingredients such as sweeteners (nutritive or nonnutritive), starch, egg and seasonings. Used in limited amounts to accompany salads and other foods. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0276 - food dressing - dressing for food (us cfr) - - - - - - - - - - Nonstandardized food product used as a meal accompaniment and consisting of a mixture of fats or oils, starch, liquid and other optional ingredients specified by the recipe; excludes condiment sauce (q.v.) and tomato or spaghetti sauce, which are vegetable products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0286 - sauce or gravy - gravy or sauce (us cfr) - - - - - - - - - - Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0289 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - USA agency food product type - - - - - - - - - - Dressing for which standards of identity are specified in the CFR. Includes french dressing (21 CFR 169.115), mayonnaise (21 CFR 169.140) and salad dressing (21 CFR 169.150). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0292 - standardized dressing (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0300 - flavor enhancer or flavoring - flavoring or flavor enhancer (us cfr) - - - - - - - - - - An acetic acid-containing liquid. Used as condiment or preservative in cooking, pickling and salad dressing preparation; may be flavored with herbs, vegetables or fruits. Natural vinegar is made by fermenting cider, wine, etc. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0302 - vinegar (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0306 - nut or seed product (us cfr) - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0316 - cheese hardness class (us cfr) - - - - - - - - - - An agency food product type is a class of food product defined by an agency or consortium. - Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0361 - This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. - agency food product type - - - - - - - - - - Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1270 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - U.S. code of federal regulations, title 21 food product type - https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl - - - - - - - - - Examples of stem vegetables are kohlrabi, celery, fennel and rhubarb. Examples of shoot vegetables are asparagus, hop, bamboo shoots and taugé. - - A vegetable having shoot or stem which can be cooked and eaten. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1005 - shoot vegetable - spear vegetable - stem or spear vegetable plant - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1006 - fruit plant used as vegetable - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1009 - polysaccharide-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1012 - sugar-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1013 - plant used for producing extract or concentrate - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1016 - starch-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1017 - oil-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1018 - vegetable-producing plant, root, tuber or bulb - - - - - - - - - - - - - - - - - - - An aquatic animal is an animal, either vertebrate or invertebrate, which lives in the water for most or all of its lifetime. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1021 - This is equivalent to: - -'fish (food source)' or 'shellfish (food source)' or 'crustacean (food source)' or 'echinoderm (food source)' or 'coelenterate (food source)' - -However, this disjunction appears to be a burden on reasoners, and so this is currently not implemented. - fish or lower water animal - - - - - - - - - - Any chemical or chemical mixture that exists in a food material or was added to a food material. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1041 - LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds). - -Note however that the LanguaL category includes additives which may be naturally derived, such as agar. - chemical food component - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1047 - grain or seed-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1048 - carbohydrate-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1057 - vegetable-producing plant, above-ground parts - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1058 - vegetable-producing plant, most parts - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1062 - temperate-zone nut producing plant - - - - - - - - - - A lime is a hybrid citrus fruit, which is typically round, lime green, 3-6 centimetres (1.2-2.4 in) in diameter, and contains acidic juice vesicles. There are several species of citrus trees whose fruits are called limes, including the Key lime (*Citrus aurantifolia*), Persian lime, kaffir lime, and desert lime. Limes are a rich source of vitamin C, sour and are often used to accent the flavours of foods and beverages. They are grown year-round. Plants with fruit called "limes" have diverse genetic origins; limes do not form a monophyletic group. [https://en.wikipedia.org/wiki/Lime_(fruit)] - http://langual.org - GRIN:10683 - ITIS:506403 - MANSFELD:7576 - PLANTS:CIAU7 - http://eol.org/pages/4414 - http://www.langual.org/langual_thesaurus.asp?termid=B1067 - Citrus aurantiifolia (Christm. & Panz.) Swingle - Citrus aurantiifolia (Christm.) Swingle - Citrus ×aurantiifolia (Christm.) Swingle (pro sp.) - citrus aurantiifolia - citrus medica var. acida - indian lime - key lime - sour lime - lime (citrus) plant - - - - - - - - - - Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. - Damion Dooley - https://en.wikipedia.org/wiki/Mammal - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1134 - mammal - - - - - - - - - - - - - - - - Suidae is a family of artiodactyl mammals which are commonly called pigs, hogs or boars. - Damion Dooley - https://en.wikipedia.org/wiki/Suidae - http://langual.org - In addition to numerous fossil species, 17 extant species are currently recognized (or 18 counting domestic pigs and wild boars separately), classified into between four and eight genera. The family includes the domestic pig, Sus scrofa domesticus or Sus domesticus, in addition to numerous species of wild pig, such as babirusas and warthogs. All suids, or swine, are native to the Old World, ranging from Asia to Europe and Africa. [Wikipedia] - - ITIS:180722 - MSW3:14200054 - http://eol.org/pages/328663 - http://www.langual.org/langual_thesaurus.asp?termid=B1136 - porcine - sus domesticus - sus scrofa - sus scrofa domesticus - Sus scrofa Linnaeus, 1758 - hog - pig - swine - - - - - - - - - - - Rutaceae, commonly known as the rue or citrus family, is a family of flowering plants, usually placed in the order Sapindales. -Citrus is a common term and genus (*Citrus*) of flowering plants in the rue family, *Rutaceae*. Citrus is believed to have originated in the part of Southeast Asia bordered by Northeastern India, Myanmar (Burma) and the Yunnan province of China. Citrus fruit has been cultivated in an ever-widening area since ancient times; the best-known examples are the oranges, lemons, grapefruit, and limes. - WIKIPEDIA:Rutaceae - http://langual.org - http://eol.org/pages/4414 - http://www.langual.org/langual_thesaurus.asp?termid=B1139 - rutaceae - citrus family - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1140 - fruit-producing plant - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1141 - white pepper - white pepper plant - - - - - - - - - - - - - - - - - - - Aquatic animals other than fish and shellfish - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1142 - aquatic invertebrate animal (excluding shellfish) - - - - - - - - - - A legume is a plant or its fruit or seed in the family *Fabaceae* (or *Leguminosae*). Legumes are grown agriculturally, primarily for their grain seed called pulse, for livestock forage and silage, and as soil-enhancing green manure. Well-known legumes include alfalfa, clover, peas, beans, chickpeas, lentils, lupin bean, mesquite, carob, soybeans, peanuts and tamarind. [https://en.wikipedia.org/wiki/Legume] - http://langual.org - http://eol.org/pages/4277 - http://www.langual.org/langual_thesaurus.asp?termid=B1156 - fabaceae - pod or seed vegetable plant - - - - - - - - - - http://langual.org - GRIN:1227 - MANSFELD:7306 - http://www.langual.org/langual_thesaurus.asp?termid=B1167 - Acer saccharum Marsh. - sugar maple plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1174 - edible seed producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1179 - flavor-producing plant - herb-producing plant - spice or flavor-producing plant - - - - - - - - - - Winter squash is an annual fruit representing several squash species within the genus Cucurbita. It differs from summer squash in that it is harvested and eaten in the mature fruit stage when the seeds within have matured fully and the skin has hardened into a tough rind. At this stage, most varieties of this fruit can be stored for use during the winter. - - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1189 - curcurbita - winter squash - Cucurbita moschata - Cucurbita pepo - cucurbita maxima - winter squash plant - - - - - - - - Californiacondor - - - - - - - - - - http://langual.org - GRIN:12606 - MANSFELD:4153 - http://www.langual.org/langual_thesaurus.asp?termid=B1190 - Cucurbita pepo L. - cucurbita pepo - yellow crookneck squash - yellow squash - summer squash plant - - - - - - - - - - http://langual.org - GRIN:28589 - MANSFELD:9964 - http://www.langual.org/langual_thesaurus.asp?termid=B1191 - Piper nigrum L. - black pepper - malabar black pepper - black pepper plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1194 - head vegetable plant - - - - - - - - - - - - - - - - - - - - - A dairy cow is an adult female member of a dairy cattle breed - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1201 - cow - domesticated cattle - dairy cow - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1208 - squash plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1213 - nut producing plant - - - - - - - - - - - Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. - Damion Dooley - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1222 - fish - fish - - - - - - - - - - - Oyster is the common name for a number of different families of salt-water bivalve molluscs that live in marine or brackish habitats. In some species the valves are highly calcified, and many are somewhat irregular in shape. -True oysters are members of the family *Ostreidae*. This family includes the edible oysters, which mainly belong to the genera *Ostrea, Crassostrea, Ostreola, Magallana, Saccostrea*. Pearl oysters are not closely related to true oysters, being members of a distinct family, the feathered oysters (*Pteriidae*). - Damion Dooley - https://en.wikipedia.org/wiki/Oyster - http://langual.org - http://eol.org/pages/2267 - http://www.langual.org/langual_thesaurus.asp?termid=B1224 - ostreidae - crassostrea spp. - ostrea spp. - pteriidae - oyster - - - - - - - - - - - http://langual.org - GRIN:33749 - ITIS:505186 - MANSFELD:10138 - PLANTS:SEOR4 - http://eol.org/pages/4428 - http://www.langual.org/langual_thesaurus.asp?termid=B1226 - simsim - Sesamum indicum L. - Sesamum orientale L. - sesamum indicum - sesamum orientale - sesame plant - - - - - - - - - - A berry is a small, pulpy, and often edible fruit. Berries are typically juicy, rounded, brightly colored, sweet or sour, and do not have a stone or pit, although many pips or seeds may be present. Common examples are strawberries, raspberries, blueberries, red currants, and blackcurrants. - The scientific usage of the term "berry" differs from common usage. In scientific terminology, a berry is a fruit produced from the ovary of a single flower in which the outer layer of the ovary wall develops into an edible fleshy portion (pericarp). The definition includes many fruits that are not commonly known as berries, such as grapes, tomatoes, cucumbers, eggplants (aubergines) and bananas. Fruits excluded by the botanical definition include strawberries, raspberries, and blackberries, which are aggregate fruits, and mulberries, which are multiple fruits. [https://en.wikipedia.org/wiki/Berry] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1231 - berry plant - - - - - - - - - - - - - - - - - http://langual.org - - GRIN:311987 - ITIS:42269 - MANSFELD:36372 - PLANTS:ZEMA - http://eol.org/pages/1115259 - http://www.langual.org/langual_thesaurus.asp?termid=B1232 - Zea mays L. - maize - zea mays - LanguaL curation note: Use 'field corn' for any breakfast cereals or snack foods having 'corn' as the main ingredient. - Zia mays plant - - - - - - - - - - - - - - - - The turkey is a large bird in the genus Meleagris, which is native to the Americas. Males of both turkey species have a distinctive fleshy wattle or protuberance that hangs from the top of the beak (called a snood). They are among the largest birds in their ranges. As in many galliformes, the male is larger and much more colorful than the female. - - http://langual.org - http://eol.org/pages/18523 - http://www.langual.org/langual_thesaurus.asp?termid=B1236 - turkey - meleagris spp. - turkey (bird) - - - - - - - - - - http://langual.org - http://eol.org/pages/2602479 - http://www.langual.org/langual_thesaurus.asp?termid=B1237 - caridea - crangonidae - palaemondidae - penaeidae - prawn - Shrimp - shrimp - - - - - - - - - - - - - - - - - - - - - - - An apple tree (Malus pumila species in genus Malus), is cultivated worldwide as a fruit tree, providing sweet, edible fruit. Malus pumila encompasses over 7,500 apple cultivars (https://en.wikipedia.org/wiki/List_of_apple_cultivars). - https://en.wikipedia.org/wiki/Apple - http://langual.org - GRIN:104681 - MANSFELD:8860 - http://eol.org/pages/8097 - http://www.langual.org/langual_thesaurus.asp?termid=B1245 - Malus domestica Borkh. - malus communis - malus domestica - pyrus malus - Malus pumila encompasses over 7,500 apple cultivars (https://en.wikipedia.org/wiki/List_of_apple_cultivars). - apple tree - - - - - - - - - - - - The taxonomies given vary widely. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1250 - capsicum - capsicum annuum - green or red pepper plant - - - - - - - - - - *Mentha* is a genus of plants in the family *Lamiaceae* (mint family). It is estimated that 13 to 18 species exist, and the exact distinction between species is still unclear. Hybridization between some of the species occurs naturally. The genus has a subcosmopolitan distribution across Europe, Africa, Asia, Australia, and North America. Mints are aromatic, almost exclusively perennial, rarely annual herbs. [https://en.wikipedia.org/wiki/Mentha] - http://langual.org - GRIN:313210 - PLANTS:MENTH - http://eol.org/pages/4302 - http://www.langual.org/langual_thesaurus.asp?termid=B1267 - Mentha - Mentha L. - Mentha spp. - mentha spp. - mint plant - - - - - - - - - - http://langual.org - GRIN:21739 - MANSFELD:30720 - http://www.langual.org/langual_thesaurus.asp?termid=B1268 - Lens culinaris Medik. - lens culinaris - lentil plant - - - - - - - - - - http://langual.org - GRIN:12617 - MANSFELD:1199 - http://www.langual.org/langual_thesaurus.asp?termid=B1274 - Cuminum cyminum L. - cuminum cyminum - cumin plant - - - - - - - - - - - The lemon, *Citrus limon *(L.) Osbeck, is a species of small evergreen tree in the flowering plant family Rutaceae, native to Asia. The tree's ellipsoidal yellow fruit is used for culinary and non-culinary purposes throughout the world, primarily for its juice, which has both culinary and cleaning uses. The pulp and rind (zest) are also used in cooking and baking. The juice of the lemon is about 5% to 6% citric acid, with a pH of around 2.2, giving it a sour taste. The distinctive sour taste of lemon juice makes it a key ingredient in drinks and foods such as lemonade and lemon meringue pie. [https://en.wikipedia.org/wiki/Lemon] - http://langual.org - GRIN:10732 - ITIS:28885 - MANSFELD:7625 - PLANTS:CILI5 - http://eol.org/pages/4414 - http://www.langual.org/langual_thesaurus.asp?termid=B1275 - Citrus limon (L.) Burm. f. - Citrus limon (L.) Burm. fil. - Citrus ×limon (L.) Burm. f. (pro sp.) - citrus limon - citrus medica var. limonum - lemon plant - - - - - - - - - - - - - - - - - The word "tomato" may refer to the plant (*Solanum lycopersicum*) or the edible, typically red, fruit that it bears. Originating in South America, the tomato was spread around the world following the Spanish colonization of the Americas, and its many varieties are now widely grown, often in greenhouses in cooler climates.See also the list of tomato cultivars - WIKIPEDIA:List_of_tomato_cultivars - http://langual.org - - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - PLANTS:SOLY2 - http://eol.org/pages/392557 - http://www.langual.org/langual_thesaurus.asp?termid=B1276 - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - gold apple - love apple - lycopersicon esculentum - lycopersicon lycopersicum - solanum lycopersicum - tomato plant - - - - - - - - - - - Kale (also called Borecole) is a form of cabbage (*Brassica oleracea* Acephala Group) in which the central leaves do not form a head. It is considered to be closer to wild cabbage than most domesticated forms. The species *Brassica oleracea* contains a wide array of vegetables, including broccoli, cauliflower, and Brussels sprouts. The Cultivar Group Acephala also includes spring greens and collard greens, which are extremely similar genetically. Kale can be classified by leaf type: Curly leaved (Scots kales), Plain leaved, Rape kale, Leaf and spear (a cross between curly leaved and plain leaved kale), Cavolo nero (also known as black cabbage, Tuscan kale, Lacinato and dinosaur kale) - WIKIPEDIA:Kale) - http://langual.org - - GRIN:319629 - ITIS:23062 - MANSFELD:23870 - http://eol.org/pages/583899 - http://www.langual.org/langual_thesaurus.asp?termid=B1281 - Brassica oleracea L. - Brassica oleracea L. var. sabellica L. - Brassica oleracea var. sabellica L. - brassica oleracea - cole - kale plant - - - - - - - - - - A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. - Damion Dooley - - http://langual.org - animal - http://www.langual.org/langual_thesaurus.asp?termid=B1297 - LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. - vertebrate animal - - - - - - - - - - - http://langual.org - GRIN:25555 - MANSFELD:11672 - http://www.langual.org/langual_thesaurus.asp?termid=B1299 - Olea europaea L. - manzanilla olive - olea europaea - olive plant - - - - - - - - - - - - The onion (*Allium cepa *L), also known as the bulb onion or common onion, is a vegetable that is the most widely cultivated species of the genus *Allium*. Its close relatives include the garlic, shallot, leek, chive,[2] and Chinese onion. - This genus also contains several other species variously referred to as onions and cultivated for food, such as the Japanese bunching onion (*Allium fistulosum*), the tree onion (*A. ×proliferum*), and the Canada onion (*Allium canadense*). The name "wild onion" is applied to a number of *Allium* species, but *A. cepa* is exclusively known from cultivation. [https://en.wikipedia.org/wiki/Onion] - http://langual.org - GRIN:300022 - PLANTS:ALLIU - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B1300 - Allium - Allium L. - Allium sp. - allium spp. - bulb onion - cebolla - garden onion - onion plant - - - - - - - - - - - Wheat (*Triticum* spp.) is a domesticated grass from the Levant that is cultivated worldwide. Major cultivated species of wheat: - - * Common wheat or Bread wheat (*Triticum aestivum*) A hexaploid species that is the most widely cultivated in the world. - - * Durum (*Triticum durum*) The only tetraploid form of wheat widely used today, and the second most widely cultivated wheat. - - * Einkorn (*Triticum monococcum*) A diploid species with wild and cultivated variants. Domesticated at the same time as emmer wheat, but never reached the same importance. - - * Emmer (*Triticum dicoccon*) A tetraploid species, cultivated in ancient times but no longer in widespread use. - - * Spelt (*Triticum spelta*) Another hexaploid species cultivated in limited quantities. - WIKIPEDIA:Wheat - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1312 - triticum spp. - wheat plant - - - - - - - - - - - - - - - - *Oryza sativa*, commonly known as Asian rice, is the plant species most commonly referred to in English as rice. *Oryza sativa* contains two major subspecies: the sticky, short-grained *japonica* or *sinica* variety, and the nonsticky, long-grained *indica* variety. - http://langual.org - GRIN:26077 - ITIS:41976 - MANSFELD:20986 - PLANTS:ORSA - http://eol.org/pages/1115098 - http://www.langual.org/langual_thesaurus.asp?termid=B1322 - lowland rice - upland rice - Rice occurs in a variety of colors, including white, brown, black, purple, and red rices. Black rice (also known as purple rice) is a range of rice types, some of which are glutinous rice. Varieties include Indonesian black rice and Thai jasmine black rice. - rice plant - - - - - - - - - - Any grass cultivated (grown) for the edible components of its grain. - Damion Dooley - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1324 - grain plant - - - - - - - - - - - - *Vitis* (grapevines) is a genus of 79 accepted species of vining plants in the flowering plant family *Vitaceae*. The genus is made up of species predominantly from the Northern hemisphere. It is economically important as the source of grapes, both for direct consumption of the fruit and for fermentation to produce wine. [https://en.wikipedia.org/wiki/Vitis] - http://langual.org - http://eol.org/pages/38383 - http://www.langual.org/langual_thesaurus.asp?termid=B1329 - Vitis - vitis spp. - grape plant - - - - - - - - - - Crustaceans form a large, diverse arthropod taxon which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill, woodlice, and barnacles. [https://en.wikipedia.org/wiki/Crustacean] - http://langual.org - http://eol.org/pages/2598871 - http://www.langual.org/langual_thesaurus.asp?termid=B1374 - crustacea - crustacean - - - - - - - - - - http://langual.org - GRIN:32617 - MANSFELD:35616 - http://www.langual.org/langual_thesaurus.asp?termid=B1378 - Saccharum officinarum L. - saccharum officinarum - sugar cane plant - - - - - - - - - - - - - Field corn is maize of varieties that (in contrast with sweet corn and popcorn) are not, in the United States, grown primarily for consumption as human food in the form of fresh kernels. More than 98% of corn-growing land in the U.S. is in use for field-corn production. Principal field corn varieties are Dent corn, Flint corn, Flour corn (including blue corn (*Zea mays amylacea*), and Waxy corn. - WIKIPEDIA:Field_corn - http://langual.org - GRIN:311987 - PLANTS:ZEMAM2 - http://eol.org/pages/8223 - http://www.langual.org/langual_thesaurus.asp?termid=B1379 - Zea mays L. ssp. mays - Zea mays L. subsp. mays - Zea mays ssp. mays L. - corn, field - dent corn - flint corn - maize - podcorn - zea mays var. indentata (not acc.) - zea mays var. indurata (not acc.) - Field corn is a general term used in North America for corn varieties other than sweet corn, popcorn, yellow food grade corn used for yellow corn meal or flour and corn starch, and white food-grade corn used for white meal or flour and corn starch. Source: https://en.wikipedia.org/wiki/Field_corn - -LanguaL curation note: Searching note--use 'field corn' for any breakfast cereal or snack food having 'corn' as the first ingredient. - field corn plant - - - - - - - - - - http://langual.org - GRIN:11523 - MANSFELD:1118 - http://www.langual.org/langual_thesaurus.asp?termid=B1381 - Coriandrum sativum L. - chinese parsley - cilantro - coriandrum sativum - coriander plant - - - - - - - - - - Lettuce (Lactuca sativa) is an annual plant of the daisy family, Asteraceae. It is most often grown as a leaf vegetable, but sometimes for its stem and seeds. - https://en.wikipedia.org/wiki/Lettuce - http://langual.org - GRIN:21360 - ITIS:36607 - PLANTS:LASA3 - http://eol.org/pages/468144 - http://www.langual.org/langual_thesaurus.asp?termid=B1390 - Lactuca sativa L. - lactuca sativa - lettuce plant - - - - - - - - - - - - - Cucumber (Cucumis sativus) is a widely cultivated plant in the gourd family, Cucurbitaceae. It is a creeping vine that bears cucumiform fruits that are used as vegetables. There are three main varieties of cucumber: slicing, pickling, and seedless. - https://en.wikipedia.org/wiki/Cucumber - http://langual.org - GRIN:12580 - MANSFELD:3698 - http://www.langual.org/langual_thesaurus.asp?termid=B1404 - Cucumis sativus L. ssp. sativus - cucumis sativus - cucumber plant - - - - - - - - - - http://langual.org - GRIN:300050 - MANSFELD:25827 - http://www.langual.org/langual_thesaurus.asp?termid=B1415 - Asparagus officinalis L. - asparagus officinalis - asparagus plant - - - - - - - - - - Turmeric is a flowering plant, Curcuma longa of the ginger family, Zingiberaceae, the roots of which are used in cooking. - - http://langual.org - GRIN:12676 - MANSFELD:3244 - http://www.langual.org/langual_thesaurus.asp?termid=B1425 - Curcuma longa L. - curcuma domestica - curcuma longa - turmeric plant - - - - - - - - - - - - The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1433 - Covers both freshwater and saltwater organisms - shellfish - - - - - - - - - - http://langual.org - ITIS:176086 - http://eol.org/pages/1049263 - http://www.langual.org/langual_thesaurus.asp?termid=B1457 - Gallus gallus (Linnaeus, 1758) - chicken - chicken - - - - - - - - - - The zucchini or courgette is a summer squash which can reach nearly a meter in length, but which is usually harvested at half that size or less. Along with certain other squashes, it belongs to the species Cucurbita pepo. Zucchini can be dark or light green. A related hybrid, the golden zucchini, is a deep yellow or orange color. - - - courgette - cucurbita pepo var. melopepo cv. zucchini - zucchini plant - - - - - - - - - - - - - - - - - - The shallot is a type of onion, specifically a botanical variety of the species *Allium cepa*. The shallot was formerly classified as a separate species,* A. ascalonicum*, a name now considered a synonym of the currently accepted name. - Like garlic, shallots are formed in clusters of offsets with a head composed of multiple cloves. The skin colour of shallots can vary from golden brown to gray to rose red, and their off-white flesh is usually tinged with green or magenta. [https://en.wikipedia.org/wiki/Shallot] - http://langual.org - - GRIN:101652 - ITIS:42720 - MANSFELD:110 - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B1538 - Allium cepa L. - Allium cepa L. var. aggregatum G. Don - Allium cepa L. var. aggregatum G.Don - allium cepa var. aggregatum - shallot plant - - - - - - - - - - - - - - - - - - This "or" class is just to represent an equivalency with a commonly used classification outside of FoodOn. It should not have subclasses under it. (2022-11-30) - http://langual.org - https://orcid.org/0000-0002-9578-0788 - http://www.langual.org/langual_thesaurus.asp?termid=B1563 - fjerkrae - gamebird - fowl - game birds - poultry or game bird - - - - - - - - - - This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1564 - This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. - food product organismal source - - - - - - - - - - Leaf vegetables, also called leafy greens, salad greens, pot herbs, vegetable greens, or simply greens, are plant leaves eaten as a vegetable, sometimes accompanied by tender petioles and shoots. - https://en.wikipedia.org/wiki/Leaf_vegetable - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1566 - leafy green - leafy vegetable plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1579 - vegetable-producing plant - - - - - - - - - - A type of fruit produced by flowering plants in the subfamily *Maloideae* of the family *Rosaceae*. - Damion Dooley - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1599 - maloideae - pome fruit plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1607 - nut or edible seed producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1643 - capsicum annuum, longum group - capsicum chile pepper - cayenne pepper - chile pepper - chili pepper - long pepper - red pepper (chile pepper) - hot pepper plant - - - - - - - - - - - - - - - - - - - A mature female chicken (usually more than 10 months of age) with meat less tender than that of a roaster, and with a nonflexible breastbone tip. - http://langual.org - hen - http://www.langual.org/langual_thesaurus.asp?termid=B1713 - stewing chicken - stewing hen - chicken hen - - - - - - - - - - The Decapoda or decapods (literally "ten-footed") are an order of crustaceans within the class Malacostraca, including many familiar groups, such as crayfish, crabs, lobsters, prawns, and shrimp. Most decapods are scavengers. [https://en.wikipedia.org/wiki/Decapoda] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1998 - decapoda - decapod - - - - - - - - - - - - - - - - - Cucurbita (Latin for gourd) is a genus of herbaceous vines in the gourd family, Cucurbitaceae, also known as cucurbits, native to the Andes and Mesoamerica. Five species are grown worldwide for their edible fruit, variously known as squash, pumpkin, or gourd depending on species, variety, and local parlance, and for their seeds. - - http://langual.org - GRIN:12957 - MANSFELD:4048 - http://www.langual.org/langual_thesaurus.asp?termid=B2091 - Cucurbita maxima L. (Duch.) - pumpkin plant - cucurbita spp. - pumpkin, squash or gourd - squash, gourd or pumpkin plant - - - - - - - - - - *Mollusca* is a large phylum of invertebrate animals whose members are known as molluscs or mollusks. Molluscs are the largest marine phylum, comprising about 23% of all the named marine organisms. Numerous molluscs also live in freshwater and terrestrial habitats. [https://en.wikipedia.org/wiki/Mollusca] - http://langual.org - EC:No 216/2009 MOL - FAO ASFIS:MOL - http://eol.org/pages/2195 - http://www.langual.org/langual_thesaurus.asp?termid=B2112 - Mollusca - mollusk - mollusc - - - - - - - - - - *Bivalvia*, in previous centuries referred to as the *Lamellibranchiata* and *Pelecypoda*, is a class of marine and freshwater molluscs that have laterally compressed bodies enclosed by a shell consisting of two hinged parts. Bivalves as a group have no head and they lack some usual molluscan organs like the radula and the odontophore. They include the clams, oysters, cockles, mussels, scallops, and numerous other families that live in saltwater, as well as a number of families that live in freshwater.[https://en.wikipedia.org/wiki/Bivalvia] - http://langual.org - http://eol.org/pages/2215 - http://www.langual.org/langual_thesaurus.asp?termid=B2113 - bivalvia - lamellibranchiata - pelecypod - pelecypoda - bivalve - - - - - - - - - - - Echinoderm is the common name given to any member of the phylum *Echinodermata* of marine animals. The adults are recognizable by their (usually five-point) radial symmetry, and include such well-known animals as sea stars, sea urchins, sand dollars, and sea cucumbers, as well as the sea lilies or "stone lilies". [https://en.wikipedia.org/wiki/Echinoderm] - http://langual.org - EC:No 1637/2001 ECH - FAO ASFIS:ECH - http://www.langual.org/langual_thesaurus.asp?termid=B2115 - Echinodermata - Echinodermata Klein, 1734 - echinodermata - echinoderm - - - - - - - - - - - - - - - - - - - Black pepper consists of unripe whole fruit that are sundried. White pepper consists of the seeds only of ripe fruit. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2255 - piper nigrum - black or white pepper plant - - - - - - - - - - - *Coelenterata* is an obsolete term encompassing the animal phyla *Cnidaria* (coral animals, true jellies, sea anemones, sea pens, and their allies) and *Ctenophora* (comb jellies). [https://en.wikipedia.org/wiki/Coelenterata] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2409 - coelenterata - coelenterate - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2559 - pepper, poblano - poblano pepper plant - - - - - - - - - - - - - - - - - - - - - - - - - The bell pepper (also known as sweet pepper or pepper in the United Kingdom, Canada and Ireland, and capsicum in Australia, India, Pakistan, Bangladesh, Singapore and New Zealand) is a cultivar group of the species *Capsicum annuum*. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". [https://en.wikipedia.org/wiki/Bell_pepper] - http://langual.org - - GRIN:311784 - GRIN:8904 - ITIS:30492 - MANSFELD:6120 - PLANTS:CAAN4 - http://eol.org/pages/581098 - http://www.langual.org/langual_thesaurus.asp?termid=B2628 - sweet pepper plant - Capsicum annuum L. - Capsicum anuum L. - capsicum frutescens var. grossum - bell pepper plant - - - - - - - - - - Unripe fruit of red or yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2629 - green pepper plant - green bell pepper plant - - - - - - - - - - Ripe fruit of red bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2630 - red bell sweet pepper plant - red sweet pepper plant - LanguaL curation note: Do not confuse with *RED PEPPER*. - red bell pepper plant - - - - - - - - - - Ripe fruit of yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2631 - yellow bell pepper plant - - - - - - - - - - Grouped together because of similar use. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2633 - paprika, hot - red pepper (pungent pepper variety) - pungent pepper variety plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B3357 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - plant according to family - - - - - - - - - - http://langual.org - CCPR: - GRIN:30008 - GRIN:300085 - PLANTS:BRASS2 - http://eol.org/pages/4219 - http://www.langual.org/langual_thesaurus.asp?termid=B3372 - Brassica - Brassica L. - Brassica sp. - Brassica spp. - brassica spp. - brassica species - - - - - - - - - - http://langual.org - CCPR: - GRIN:12546 - http://www.langual.org/langual_thesaurus.asp?termid=B3407 - Cucumis sativus L.; pickling cucumber cultivars - bur cucumber - bur gherkin - cucumis anguria - west indian gherkin plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4168 - plant used for dietary supplements - - - - - - - - - - *Allium* is a genus of monocotyledonous flowering plants that includes hundreds of species, including the cultivated onion, garlic, scallion, shallot, leek, and chives. [https://en.wikipedia.org/wiki/Allium] - http://langual.org - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B4302 - allium - onion - wild onion - allium species - - - - - - - - - - The biological subfamily *Bovinae* includes a diverse group of 10 genera of medium- to large-sized ungulates, including domestic cattle, the bison, African buffalo, the water buffalo, the yak, and the four-horned and spiral-horned antelopes. The evolutionary relationship between the members of the group is obscure, and their classification into loose tribes rather than formal subgroups reflects this uncertainty. General characteristics include cloven hoofs and usually at least one of the sexes of a species having true horns. - WIKIPEDIA:Bovinae - http://langual.org - http://eol.org/pages/2851454 - http://www.langual.org/langual_thesaurus.asp?termid=B4374 - bovinae - bovine - - - - - - - - - - A bovid (family *Bovidae*) is any of almost 140 species of cloven-hoofed, ruminant mammal which has males with characteristic unbranching horns covered in a permanent sheath of keratin. - -The family is widespread, being native to Asia, Africa, Europe and North America, and diverse: members include bison, African buffalo, water buffalo, antelopes, gazelles, sheep, goats, muskoxen, and domestic cattle. - WIKIPEDIA:Bovidae - http://langual.org - http://eol.org/pages/7687 - http://www.langual.org/langual_thesaurus.asp?termid=B4381 - bovidae - bovid - - - - - - - - - - *Cucumis* is a genus of twining, tendril-bearing plants in the *Cucurbitaceae* family which includes the cucumber (*Cucumis sativus*), muskmelons (*Cucumis melo*, including cantaloupe and honeydew), the horned melon (*Cucumis metuliferus*), and the West Indian gherkin (*Cucumis anguria*). [https://en.wikipedia.org/wiki/Cucumis] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4459 - cucumis species - - - - - - - - - - The *Cucurbitaceae*, also called cucurbits and the gourd family, are a plant family consisting of about 965 species in around 95 genera, the most important of which are: - *Cucurbita* - squash, pumpkin, zucchini, some gourds; - *Lagenaria* - calabash, and others that are inedible; - *Citrullus* - watermelon (*C. lanatus, C. colocynthis*) and others; - *Cucumis* - cucumber (*C. sativus*), various melons; - *Luffa* - luffa, loofah - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4460 - cucurbitaceae - gourd/squash family - - - - - - - - - - Tunicates, previously known as *Urochordata* or urochordates, are members of the *Tunicata*, a subphylum of the phylum *Chordata*. They are marine filter feeders with a saclike morphology. In their respiration and feeding they take in water through an incurrent (or inhalant) siphon and expel the filtered water through an excurrent (or exhalant) siphon. Most adult tunicates are sessile and attached to rocks or similarly suitable surfaces on the ocean floor; others such as salps, doliolids and pyrosomes swim in the pelagic zone as adults. Various species are commonly known as sea squirts or sea pork. - WIKIPEDIA:Tunicate - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4466 - oopah - sea squirt - tunicata - tunicate - - - - - - - - - - Pattypan squash, sunburst squash, cibleme in Cajun French, white squash, scallopini or yellow squash in Australian English, is a summer squash (species *Cucurbita pepo*) notable for its small size, round and shallow shape, and scalloped edges, somewhat resembling a small toy top, or flying saucer. - WIKIPEDIA:Pattypan_squash - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B4505 - pattypan squash plant - scallop squash plant - - - - - - - - - - The *Solanaceae*, or nightshades, are an economically important family of flowering plants. Many members of the family contain potent alkaloids, and some are highly toxic, but many, including tomatoes, potatoes, eggplant, bell/chili peppers, and tobacco are widely used. The *Solanaceae* consists of about 98 genera and some 2,700 species, with a great diversity of habitats, morphology and ecology. [https://en.wikipedia.org/wiki/Solanaceae] - http://langual.org - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B4934 - nightshade family - solanaceae plant - - - - - - - - - - *Solanum* is a large and diverse genus of flowering plants, which include two food crops of high economic importance, the potato and the tomato. It also contains the nightshades and horse nettles, as well as numerous plants cultivated for their ornamental flowers and fruit. - *Solanum* species show a wide range of growing habits, such as annual and perennials, vines, subshrubs, shrubs, and small trees. Many formerly independent genera like *Lycopersicon* (the tomatoes) and *Cyphomandra* are now included in *Solanum* as subgenera or sections. Thus, the genus today contains roughly 1,500-2,000 species. - - http://langual.org - GRIN:300568 - PLANTS:SOLAN - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B5104 - Solanum - Solanum L. - Solanum spp. - solanum plant - - - - - - - - - - - - - - - - - - Edible flesh of any type of animal, including poultry and seafood. Excludes parts containing only animal fat, which is indexed under *FAT OR OIL* or under *FAT, TRIM*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0103 - Damion Dooley Feb 6, 2017: Good meat cut resources to incorporate for Canada: The CFIA Meat Cuts Manual -http://www.inspection.gc.ca/food/labelling/meat-cuts/eng/1300126276015/1300126372856 - meat part of animal - - - - - - - - - - A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0108 - sugar - sugar - - - - - - - - - - Anatomical part of the plant or animal from which a food product or its major ingredient is derived. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0116 - LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." - part of organism - - - - - - - - - - Bone, feathers, shell, skin or trim fat. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0122 - LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. - nonmeat part of animal - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0125 - boneless meat - skeletal meat part, without bone, skin undetermined - skeletal meat part, without bone or shell - - - - - - - - - - Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0127 - LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - animal body or body part - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0138 - LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED* in LanguaL 2008. - fruit, peel removed - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0144 - LanguaL curation note: This broad term is used for the plant as a whole, excluding the root and the fruit; for any piece consisting of two or more individual parts (e.g., a celery stalk with the leaf blades attached); or for any mixture of two or more individual parts (e.g., mushroom stems and pieces). - plant above surface, excluding fruit and seed - - - - - - - - - - The parts of a plant that are not fruit or seed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0148 - flower, root, stem or leaf - leaf, flower, root or stem - stem, leaf, flower or root - root, stem, leaf or flower - - - - - - - - - Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0152 - carbohydrate extract, concentrate, or isolate - - - - - - - - - - - - - - - - - - - - - - - Soft sugar whose crystals are covered by a film of refined dark syrup that imparts color, flavor, and moisture. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0156 - brown sugar - brown sugar - - - - - - - - - - - - - - - - - White sugar is highly refined crystalline sugar, mostly sucrose, that appears white in color. White sugar is commonly used in North America and Europe, made either of beet sugar or cane sugar, that has undergone a refining process which removes molasses. - Damion Dooley - https://en.wikipedia.org/wiki/White_sugar - http://langual.org - 2019-06-18T21:52:36Z - https://upload.wikimedia.org/wikipedia/commons/thumb/0/04/A_Bowl_of_Sugar_2.jpg/320px-A_Bowl_of_Sugar_2.jpg - SUBSET_SIREN:F4298 - http://www.langual.org/langual_thesaurus.asp?termid=C0157 - subset_siren - SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157) - - white sugar - white sugar - - - - - - - - - - Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0164 - part of animal - - - - - - - - - - - - - - - - - - - - - - The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0167 - berry - berry or fruit (anatomical part) - fruit or berry, peel undetermined - hip (fruit) - infructescence - LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. - -Renamed from *FRUIT OR BERRY* in LanguaL 2008. - fruit part - - - - - - - - - - - Carcass meat from any type of animal including poultry and seafood. Includes retail and wholesale cuts other than organ meat. Refers to the whole carcass or parts. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0175 - skeletal meat part - - - - - - - - - - - - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0178 - seed part - - - - - - - - - - Poultry, game bird or turtle eggs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0194 - LanguaL curation note: Fish roe are indexed under *OVARY, ROE*. - egg or egg component - - - - - - - - - - Edible organ meat, including blood and bone marrow. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0218 - variety meat - organ meat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The egg yolk and albumen component of one or more eggs with shell removed. - Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0225 - egg (without shell) - - - - - - - - - - A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0228 - Damion Dooley's note: Items in this branch will be merged into foodon food product branch. - extract, concentrate or isolate of plant or animal - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0229 - flesh of fruit - LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED, CORE, PIT OR SEED REMOVED* in LanguaL 2008. - fruit, peel removed, core, pit or seed removed - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0238 - bulb, root or tuber - tuber, bulb or root - root, tuber or bulb - - - - - - - - - - The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0307 - seed oil - - - - - - - - - - The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0113 - Damion Dooley's note: these categories need to be mapped over to PATO phenotypic categories, with a suitable treatment of mixtures of solids that are divided into parts. - food physical quality - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0122 - LanguaL curation note: The distinctions in this category are based on size characteristics, primarily thickness, which are important for heat transfer and for diffusion of chemicals in processing. *DIVIDED INTO HALVES, QUARTERS OR SEGMENTS* should be examined first and if one of the descriptors listed applies it should be used regardless of the size of the pieces. If none of these are applicable, other *DIVIDED OR DISINTEGRATED* descriptors should be examined. Do not use any of these descriptors if dividing or disintegrating results in a semiliquid or semisolid product. - divided or disintegrated - - - - - - - - - - - - - - - - - - - - - - - - - - - A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. - http://langual.org - SUBSET_SIREN:F5105 - http://www.langual.org/langual_thesaurus.asp?termid=E0130 - fluid - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - food (liquid) - - - - - - - - - - - - - - - - - - - - - - - - - - - A solid product is a hard or soft product capable of retaining its own shape at room temperature (20 degrees C.). A soft product that is spreadable or formable is considered semisolid. - http://langual.org - SUBSET_SIREN:F17643 - http://www.langual.org/langual_thesaurus.asp?termid=E0151 - solid - food (solid) - - - - - - - - - - Divided into pieces whose shape bears little or no relation to the shape of the whole. If all dimensions are below 0.2 cm., use *DISINTEGRATED OR GROUND*. Examples are: bread slice, cubed beef, sliced carrot, cut green beans, apple ring, shredded cabbage or cheese. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0152 - divided into pieces - - - - - - - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=G0002 - food cooking - - - - - - - - - Cooked at moderate to high levels of heat in which no liquid is added and only small amounts of fat may be added to prevent sticking. - http://www.langual.org/langual_thesaurus.asp?termid=G0004 - dry cooked - LanguaL - cooking by dry heat - - - - - - - - - - - - - - - Cooked without moisture, covered or uncovered, in an oven. - Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=G0005 - roasting - food baking - - - - - - - - - Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. - http://www.langual.org/langual_thesaurus.asp?termid=H0111 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - food treatment process - - - - - - - - - A food modification process by microbial or enzymatic action which results in molecular changes in any food component. - http://www.langual.org/langual_thesaurus.asp?termid=H0119 - fermented, unspecified - LanguaL curation note: If salt, sugar or other food additive is used to aid in the modification process, index it by the appropriate term under *INGREDIENT ADDED*. - microbial/enzymatic modification process - - - - - - - - - A food modification process where physical or chemical changes are effected in any food ingredient through a physical or non-enzymatic chemical process. - http://www.langual.org/langual_thesaurus.asp?termid=H0130 - physical/chemical modification process - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=H0141 - LanguaL curation note: Used when the food product underwent mechanical, chemical or enzymatic modification that has affected the texture, flavor or other characteristic of the product. - food modification process - - - - - - - - - - - - - - - - - - - - - - requires curation - A food product which is output of a salting process where salt is dissolved or absorbed into the food as an ingredient or flavourant. - http://langual.org - - - http://www.langual.org/langual_thesaurus.asp?termid=H0173 - salted - compounded food - LanguaL curation note: Used when it is necessary to distinguish one product from another (e.g., salted vs. unsalted peanuts), or for salt-fermented products (e.g. soy sauce). It can also be used for other products known to contain at least 4% added and naturally present salt (sodium chloride). -When salting is used as preservation method, index *preservation by SALTING [J0103]* or narrower term. - food (salted) - salted - - - - - - - - - - - - - - - - - - This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred. - nut or seed added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0177 - LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. - plant seed or nut food product - - - - - - - - - Treated with acid that may be produced by fermentation or added and/or with salt brine, often in the presence of spices or herbs, producing changes in flavor and texture. - http://www.langual.org/langual_thesaurus.asp?termid=H0190 - LanguaL curation note: Also index by other applicable terms from *MICROBIALLY/ ENZYMATICALLY MODIFIED*. - pickling - - - - - - - - - - - - - - - - - - A fat or oil derived from vegetable material - Damion Dooley - vegetable fat or oil added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0263 - This is a convenience class inherited from LanguaL - vegetable fat or oil - - - - - - - - - Preservation by adding chemical preservatives (e.g., sorbic acid, sodium benzoate, BHT, calcium proprionate) to suppress or inhibit undesirable microorganisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0100 - preservation by adding chemicals - - - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0103 - LanguaL curation note: Used when salting is used for preservation. The salt content of the food is generally 8% or higher (e.g. salted fish, etc.). - food salting - - - - - - - - - The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. - http://www.langual.org/langual_thesaurus.asp?termid=J0107 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - food preservation process - - - - - - - - - Preservation by use of chemical to destroy, suppress or inhibit undesirable microorganisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0109 - chemical food preservation process - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0119 - LanguaL curation note: Used when sufficient radiation (e.g. 10 kGy) is applied to destroy most patho-genic and food spoilage organisms. Also index *preservation by CHILLING*. - pasteurization by irradiation - - - - - - - - - Preservation by the use of high temperature for a time sufficient to reduce or destroy undesirable microorganisms and enzyme activity. [FDA CFSAN 1995] - http://www.langual.org/langual_thesaurus.asp?termid=J0120 - heat treatment food preservation - - - - - - - - - Preservation by irradiation, primarily by gamma radiation. - http://www.langual.org/langual_thesaurus.asp?termid=J0122 - preservation by ionizing radiation - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0135 - LanguaL curation note: Used when the product is held at a temperature of 60-150 °C (140-300 °F) for a time sufficient to destroy most pathogenic and food spoilage organisms. When followed by refrigeration, also index *preservation by CHILLING*. - pasteurization by heating - - - - - - - - - Preservation by the use of radiation to destroy or suppress undesirable microorganisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0138 - preservation by irradiation - - - - - - - - - Preservation method that lowers the water activity (relative humidity) of a food product. This is accomplished by using mechanical dehydration equipment, by natural drying, by adding salt, sugar or other agents to the food or by surface drying during a refrigeration or freezing operation. This method of preservation may be used in conjunction with other preservation methods such as preservation by thermal processing. - http://www.langual.org/langual_thesaurus.asp?termid=J0145 - preservation by reducing water activity - - - - - - - - - http://www.langual.org/langual_thesaurus.asp?termid=J0149 - preservation by adding acid - - - - - - - - - Preservation by adding inorganic acids or salts (e.g. SO2, H2SO4, KNO4, NaNO3) to suppress or inhibit undesirable micro-organisms or enzyme activity. - http://www.langual.org/langual_thesaurus.asp?termid=J0154 - preservation by adding inorganic acids or salts - - - - - - - - - - A food contact material which encloses the food and can be in the type of a container, packaging or wrapping. - Previous definition was a legacy definition, not ontological and has been moved to comments. - http://orcid.org/0000-0001-8008-8249 - https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/food-packaging - http://langual.org - container - packaging - wrapping - http://www.langual.org/langual_thesaurus.asp?termid=M0100 - food container - food wrap - food wrapping - Previous definition: Type of container or wrapping defined by the main container material, the container form and the material of the liner lids of ends. Also type of container or wrapping by form; prefer description by material first, then by form. [FDA CFSAN 1995]. - food packaging - - - - - - - - - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0194 - bottle, jar or can - jar, bottle or can - can, bottle or jar - - - - - - - - - - Classification corresponding to FSTA Thesaurus Packaging 3.1 Package Types - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0195 - container or wrapping by form - - - - - - - - - - - - - - - - - - - - A container which is a bottle or a jar. - https://en.wikipedia.org/wiki/Container - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=M0203 - jar - bottle or jar - - - - - - - - - - A container which is made of a thin metal and and is used for the distribution or storage of goods. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=M0204 - canister - canned (packed in a can) - can (container) - - - - - - - - - - - A narrow-necked container typically made of glass or plastic that is used to store and transport liquids. - https://en.wikipedia.org/wiki/Bottle - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=M0214 - bottle - - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0215 - wide-necked bottle - wide-necked jar - jar - jar - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=M0218 - jug or demijohn - - - - - - - - - - The specific container or coating materials in direct contact with the food. [FDA CFSAN 1995] - - - http://langual.org - surface - http://www.langual.org/langual_thesaurus.asp?termid=N0010 - food product contact surface - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=N0050 - food contact surface from natural material - - - - - - - - - - - An uncured cheese food product which is soft and acid set and can be made from cow or buffalo milk. - https://en.wikipedia.org/wiki/Paneer - 2022-10-20T17:11:49.301Z - https://orcid.org/0000-0001-5193-0062 - https://orcid.org/0000-0001-8008-8249 - - ponir - paneer - paneer - - - - - - - - - requires discussion - An avian animal which is any of a number of species of wild birds which are hunted, killed and eaten by humans. - https://simple.wikipedia.org/wiki/Game_bird#:~:text=A%20game%20bird%20is%20any,so%20there%20are%20gun%20laws. - - 2022-11-03T01:40:18.746Z - game bird - - - - - - - - - Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data - - ancestral group - ancestry category - - - - - - - - - Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap -BEB, GIH, ITU, PJL and STU populations. - - South Asian - - - - - - - - - Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations. - - South East Asian - - - - - - - - - Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. - - Asian unspecified - Asian - - - - - - - - - Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations -from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations - Jackie MacArthur - Joannella Morales - - Hispanic or Latin American - - - - - - - - - - Mexican - Mexican - - - - - - - - - - American - American - - - - - - - - - - Asian Indian - Indian Asian - Indian - Indian - - - - - - - - - - Thai - Thai - - - - - - - - - Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American - - undefined ancestry population - - - - - - - - - data item - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - - data item - - - - - - - - - symbol - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - based on Oxford English Dictionary - - symbol - - - - - - - - - information content entity - - A generically dependent continuant that is about some thing. - PERSON: Chris Stoeckert - OBI_0000142 - - information content entity - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - - curation status specification - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - - data about an ontology part - - - - - - - - - - Benincaseae - - - - - - - - - - bony vertebrates - Euteleostomi - - - - - - - - - - stalk celery plant - - http://langual.org - GRIN:102051 - ITIS:182185 - MANSFELD:1236 - PLANTS:APGRD - http://eol.org/pages/1245043 - http://www.langual.org/langual_thesaurus.asp?termid=B3729 - celery - stalk celery - Apium graveolens L. var. dulce (Mill.) DC. - Apium graveolens var. dulce (Mill.) Pers. - Apium graveolens var. dulce (P. Mill.) DC. - apium graveolens var. dulce - Apium graveolens Dulce Group - - - - - - - - - - Archelosauria - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - - turmeric - Curcuma longa - - - - - - - - - - Boreoeutheria - - - - - - - - - - Acrogymnospermae - - - - - - - - - - Mesangiospermae - - - - - - - - - - Petrosaviidae - - - - - - - - - - Pentapetalae - - - - - - - - - - Panicoideae - - - - - - - - - - PACMAD clade - - - - - - - - - - Oryzeae - - - - - - - - - - Andropogoneae - - - - - - - - - - Galloanserae - - - - - - - - - - Fabeae - - - - - - - - - - Andropogonodae - - - - - - - - - - walnut family - Juglandaceae - - - - - - - - - - - *Juglans* is a plant genus of the family *Juglandaceae*, the seeds of which are known as walnuts. - - WIKIPEDIA:Juglans - - http://langual.org - 2022-02-01T00:18:43Z - http://eol.org/pages/38394 - http://www.langual.org/langual_thesaurus.asp?termid=B1290 - walnuts - juglans spp. - LanguaL curation note: When indexing the walnut fruit (drupe, seed) index both *WALNUT [B1290]* and *FRUIT [C0167]* (or its more precise narrower terms). - Juglans - - - - - - - - - - Amygdaloideae - - - - - - - - - - Aurantioideae - - - - - - - - - - NPAAA clade - - - - - - - - - - 50 kb inversion clade - - - - - - - - - - Hologalegina - - - - - - - - - - IRL clade - - - - - - - - - - magnoliids - Magnoliidae - - - - - - - - - - rue family - Rutaceae - - - - - - - - - - Apioideae - - - - - - - - - - apioid superclade - - - - - - - - - - Scandiceae - - - - - - - - - - Apieae - - - - - - - - - - Daucinae - - - - - - - - - - Citrus - - - - - - - - - - Citrus x limon - lemon - Citrus limon - - - - - - - - - - eucaryotes - eukaryotes - Eukaryota - - - - - - - - - - Bovinae - - - - - - - - - - - "Miller intended Malus pumila (from the Latin pumilus – small) to denote the Paradise Apple, a weak, low-growing form of M. domestica used as a rootstock, which he took to be a distinct species (Bean 1981). Until very recently it has been widely used for all forms of orchard apple (otherwise known as M. domestica), and sometimes also for their primary wild progenitor (for example by Juniper & Mabberley 2006; Grimshaw & Bayton 2009). While M. pumila is the earlier name, M. domestica has been conserved (Qian et al. 2010, Applequist 2017)." - from https://treesandshrubsonline.org/articles/malus/malus-domestica/ - paradise apple plant - - http://langual.org - GRIN:23261 - ITIS:25262 - PLANTS:MAPU - http://eol.org/pages/629943 - http://www.langual.org/langual_thesaurus.asp?termid=B3346 - paradise apple - ping guo - Malus pumila Mill. - Malus pumila P. Mill. - malus pumila - malus pumila var. niedzwetzkyana - malus sylvestris var. niedzwetskyana - malus sylvestris var. paradisiaca - Malus pumila - - - - - - - - - - shallot - Allium cepa var. aggregatum - - - - - - - - - - Laurasiatheria - - - - - - - - - - tetrapods - Tetrapoda - - - - - - - - - - amniotes - Amniota - - - - - - - - - - Theria - Theria <mammals> - - - - - - - - - - diapsids - Sauria - - - - - - - - - - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group - green plants - Viridiplantae - - - - - - - - - - Opisthokonta - - - - - - - - - - Bilateria - - - - - - - - - - deuterostomes - Deuterostomia - - - - - - - - - - Gnetaceae - - - - - - - - - - Gnetum - - - - - - - - - - angiosperms - flowering plants - Magnoliopsida - - - - - - - - - - Laurales - - - - - - - - - - laurel family - Lauraceae - - - - - - - - - - avocado - Persea americana - - - - - - - - - - Fagales - - - - - - - - - - Pecora - - - - - - - - - - BEP clade - BOP clade - - - - - - - - - - Apiineae - - - - - - - - - - cucumber family - Cucurbitaceae - - - - - - - - - - Cucumis - - - - - - - - - - cucumber - cucumbers - Cucumis sativus - - - - - - - - - - marrows - pumpkins - squashes - Cucurbita - - - - - - - - - - - - - - - http://langual.org - GRIN:12606 - ITIS:22373 - PLANTS:CUPE - Cucurbita pepo L. - Cucurbita pepo - - - - - - - - - - Brassicales - - - - - - - - - - Cruciferae - mustard family - Brassicaceae - - - - - - - - - - Brassica - - - - - - - - - - Rosales - - - - - - - - - - rose family - Rosaceae - - - - - - - - - - Malus - - - - - - - - - - apple - apple tree - cultivated apple - Malus domestica - - - - - - - - - - Prunus - - - - - - - - - - pea family - Fabaceae - - - - - - - - - - Indian corn - Zea mays subsp. sacharata - corn - maize - Zea mays subsp. mays - - - - - - - - - - Papilionoideae - - - - - - - - - - lentil - Lens culinaris - - - - - - - - - - Poales - - - - - - - - - - carrot family - Apiaceae - - - - - - - - - - Daucus - - - - - - - - - - Queen Anne's lace - carrot - carrots - Daucus carota - - - - - - - - - - - A marshland plant in the family Apiaceae that has been cultivated as a vegetable since antiquity. - - celery plant - - - GRIN:300034 - MANSFELD:1212 - http://www.langual.org/langual_thesaurus.asp?termid=B1282 - Apium graveolens L. - Apium graveolens - - - - - - - - - - asparagus family - Asparagaceae - - - - - - - - - - mammals - Mammalia - - - - - - - - - - Solanales - - - - - - - - - - nightshade family - Solanaceae - - - - - - - - - - peppers - Capsicum - - - - - - - - - - - ancho pepper plant - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2550 - C annuum - Capsicum annuum - - - - - - - - - - - WIKIPEDIA:Tomato - - http://langual.org - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - http://eol.org/pages/392557 - tomato - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - lycopersicon esculentum - Solanum lycopersicum - - - - - - - - - - Solanum - - - - - - - - - - Sapindales - - - - - - - - - - Solanoideae - - - - - - - - - - monocots - monocotyledons - Liliopsida - - - - - - - - - - grass family - Poaceae - - - - - - - - - - Gnetum africanum - - - - - - - - - - Oryza - - - - - - - - - - - Asian cultivated rice - asian rice - red rice - rice - Oryza sativa - - - - - - - - - - maize - FoodOn Note: the NCBITaxon exact synonym "maize" is more appropriate for "Zea mays subsp. mays" - Zea mays - - - - - - - - - - Zingiberales - - - - - - - - - - ginger family - Zingiberaceae - - - - - - - - - - Zingiber - - - - - - - - - - amaryllis family - Amaryllidaceae - - - - - - - - - - Allium - - - - - - - - - - - - http://langual.org - GRIN:2244 - ITIS:42720 - PLANTS:ALCE - http://eol.org/pages/8187 - onion - Allium cepa L. - pickling onion - allium cepa - Allium cepa - - - - - - - - - - - - - Garlic (*Allium sativum*) is a species in the onion genus, *Allium*.Its close relatives include the onion, shallot, leek, chive, and Chinese onion. Garlic is native to Central Asia and northeastern Iran, and has long been a common seasoning worldwide, with a history of several thousand years of human consumption and use. [https://en.wikipedia.org/wiki/Garlic] - garlic plant - - http://langual.org - GRIN:2368 - GRIN:315611 - ITIS:42652 - MANSFELD:212 - PLANTS:ALSA2 - http://eol.org/pages/1084926 - http://www.langual.org/langual_thesaurus.asp?termid=B1233 - garlic - Allium sativum L. - allium sativum - Allium sativum - - - - - - - - - - Asparagus - - - - - - - - - - garden asparagus - Asparagus officinalis - - - - - - - - - - commelinids - - - - - - - - - - cumin - Cuminum cyminum - - - - - - - - - - vascular plants - Tracheophyta - - - - - - - - - - seed plants - Spermatophyta - - - - - - - - - - Eumetazoa - - - - - - - - - - Asteridae - asterids - - - - - - - - - - rosids - - - - - - - - - - Fabales - - - - - - - - - - Maleae - - - - - - - - - - Asparagales - - - - - - - - - - chordates - Chordata - - - - - - - - - - Vertebrata - vertebrates - Vertebrata <vertebrates> - - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrates> - - - - - - - - - - euphyllophytes - Euphyllophyta - - - - - - - - - - Archosauria - - - - - - - - - - birds - avian - Aves - - - - - - - - - - Neognathae - - - - - - - - - - landfowls - Galliformes - - - - - - - - - - turkeys - Phasianidae - - - - - - - - - - Gallus domesticus - bantam - chicken - chickens - gallus gallus domesticus - Gallus gallus - - - - - - - - - - Phasianinae - - - - - - - - - - Meleagris - - - - - - - - - - whales, hippos, ruminants, pigs, camels etc. - Artiodactyla - - - - - - - - - - fabids - - - - - - - - - - malvids - - - - - - - - - - campanulids - - - - - - - - - - lamiids - - - - - - - - - - eutherian mammals - placental mammals - placentals - Eutheria - - - - - - - - - - ginger - Zingiber officinale - - - - - - - - - - Brassiceae - - - - - - - - - - boars - pigs - Suidae - - - - - - - - - - - A suid native to much of Eurasia and North Africa. - - Damion Dooley - - - http://langual.org - 2020-04-01T23:10:20Z - pig - pigs - swine - wild boar - Sus scrofa - - - - - - - - - - Bovidae - - - - - - - - - - oxen, cattle - Bos - - - - - - - - - - Cattle (colloquially cows) are the most common type of large domesticated ungulates. They are a prominent modern member of the subfamily *Bovinae*, are the most widespread species of the genus *Bos*, and are most commonly classified collectively as *Bos taurus*... with three subspecies: *Bos taurus primigenius, Bos taurus indicus, Bos taurus taurus*. - cattle - - - - - ITIS:183838 - MSW3:14200687 - Bos taurus Linnaeus, 1758 - bovine - cattle - cow - dairy cow - domestic cattle - domestic cow - ox - oxen - Bos taurus - - - - - - - - - - - Curcuma - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - - - processed material - - - - - - - - - organism - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - WEB: http://en.wikipedia.org/wiki/Organism - - organism - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - - quality - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. - - quality of a solid - - - - - - - - - A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. - - quality of a liquid - - - - - - - - - A quality inhering in a bearer by virtue of its constitution. - - quality of a substance - - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - - genet (broad) - ramet (broad) - - PO_GIT:538 - PO_GIT:69 - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - plant_anatomy - clonal colony (related) - colony (related) - PO:0000003 - - - Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). - whole plant - - - - - - - - - - - - - - - - - - - - - A phyllome primordium (PO:0025128) that develops from a vascular leaf anlagen (PO:0025431) and is part of a vegetative shoot apex (PO:0025223) and is committed to the development of a vascular leaf (PO:0009025). - - PO_GIT:466 - leaf primordium (exact) - portion of vascular leaf primordium tissue (exact) - primordio de hoja (Spanish, exact) - vascular leaf primordia (exact, plural) - 葉原基 (Japanese, exact) - plant_anatomy - PO:0000017 - vascular leaf primordium - - - - - - - - - A floral structure primordium (PO:0025477) that is committed to the development of an ovule (PO:0020003). - - PO_GIT:465 - portion of ovule primordium tissue (exact) - primordio de &#243vulo (Spanish, exact) - 胚珠原基（可視的） (Japanese, exact) - plant_anatomy - PO:0000018 - The transition from ovule primordium to ovule occurs when an integument (PO:0020021) begins to develop from the protoderm (PO:0006210). - ovule primordium - - - - - - - - - A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062). - - PO_GIT:465 - pistil primordium (exact) - portion of gynoecium primordium tissue (exact) - primordio de gineceo (Spanish, exact) - 雌蕊原基(可視的） (Japanese, exact) - plant_anatomy - PO:0000019 - Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030). - gynoecium primordium - - - - - - - - - A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). - - PO_GIT:234 - &#225pice del epiblasto (epiblastema) (Spanish, exact) - シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0000037 - - shoot axis apex - - - - - - - - - A root (PO:0009005) that is initiated in a developing plant embryo (PO:0009009). - - PO_GIT:594 - embryonic root (exact) - ra&#237z embri&#243nica (Spanish, exact) - 初期の根、胚根 (Japanese, exact) - plant_anatomy - PO:0000045 - - embryo root - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) which is the organogenic region of the meristem, characterized by higher rates of cell division. - - zona perif&#233rica (Spanish, exact) - 周辺帯 (Japanese, exact) - plant_anatomy - peripheral meristem (related) - PO:0000225 - peripheral zone - - - - - - - - - A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395). - - PO:0006329 - PO:0006373 - PO:0006374 - PO:0025091 - floral meristem (exact) - mersitema floral (Spanish, exact) - 花芽分裂組織 (Japanese, exact) - Poaceae floret meristem (narrow) - ear floret meristem (narrow) - floret meristem (narrow) - tassel floret meristem (narrow) - plant_anatomy - floral apical meristem (related) - PO:0000229 - In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). - flower meristem - - - - - - - - - A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. - - CL:0000034 - PO_GIT:272 - c&#233lula meristem&#225tica (Spanish, exact) - stem cell (exact) - 分裂組織細胞 (Japanese, exact) - plant_anatomy - PO:0004010 - - meristematic cell - - - - - - - - - - - - - - - A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). - - PO_GIT:467 - portion of root primordium tissue (exact) - primordio de ra&#237z (Spanish, exact) - root primordia (exact, plural) - 根原基（可視的） (Japanese, exact) - plant_anatomy - PO:0005029 - A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). - root primordium - - - - - - - - - - - - - - - - - - - - - A lateral plant organ (PO:0009008) produced by a shoot apical meristem (PO:0020148). - - filoma (Spanish, exact) - フィロム、葉(的）器官 (Japanese, exact) - plant_anatomy - PO:0006001 - - - phyllome - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). - - PO_GIT:472 - PO_GIT:583 - meristema del epiblasto (epiblastema) (Spanish, exact) - シュート分裂組織 (Japanese, exact) - plant_anatomy - PO:0006079 - - shoot system meristem - - - - - - - - - A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). - - PO_GIT:125 - portion of protoderm tissue (exact) - protodermis (Spanish, exact) - 前表皮、原表皮 (Japanese, exact) - plant_anatomy - dermatogen cell (related) - PO:0006210 - A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. - protoderm - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). - - PO_GIT:390 - plant_structure_development_stage - Solanaceae whole plant growth stages (SGN:0000001) (related) - cereal plant growth stage ontology (GRO:0007199) (related) - maize growth stage (GRO:0007002) (related) - plant growth stages in Arabidopsis (TAIR:0000021) (related) - rice growth stage (GRO:0007040) (related) - sorghum growth stage (GRO:0007124) (related) - wheat, barley and oat growth stage (GRO:0007156) (related) - PO:0007033 - - whole plant development stage - - - - - - - - - A shoot apical meristem (PO:0020148) that gives rise to the apical growth of vegetative tissues and organs. - - PO_GIT:36 - meristema vegetativo apical del epiblasto (epiblastema) (Spanish, exact) - 栄養シュート頂端分裂組織 (Japanese, exact) - plant_anatomy - vegetative meristem (related) - PO:0008016 - vegetative shoot apical meristem - - - - - - - - - - - - - - - A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs. - - PO_GIT:36 - meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂端 分裂組織 (Japanese, exact) - plant_anatomy - PO:0008028 - reproductive shoot apical meristem - - - - - - - - - - - - - - - A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). - - PO:0020067 - PO:0020068 - PO:0020069 - PO:0020070 - PO:0020071 - PO:0020072 - PO:0020073 - PO:0020074 - PO:0020076 - PO:0020077 - PO:0020078 - PO:0020079 - PO:0020080 - PO:0020082 - PO:0020083 - PO:0020087 - PO:0020107 - aggregate fruit (broad) - compound fruit (broad) - dehiscent fruit (broad) - diaspore (broad) - indehiscent fruit (broad) - multiple fruit (broad) - propagule (broad) - PO_GIT:76 - frucht (exact, German) - fruto (exact, Spanish) - 果実 (exact, Japanese) - coenocarp (narrow) - syncarp (narrow) - plant_anatomy - PO:0009001 - - - - - - - A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. - fruit - https://en.wikipedia.org/wiki/Fruit_anatomy - - - - - - - - - A cell which is a plant structure (PO:0009011). - - cell (broad) - GO:0005623 - PO_GIT:56 - c&#233lula vegetal (Spanish, exact) - 植物細胞 (Japanese, exact) - plant_anatomy - PO:0009002 - - - - Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. - plant cell - - - - - - - - - - - - - - - - - - - - - A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. - - PO:0003006 - PO_GIT:578 - ra&#237z (Spanish, exact) - radices (exact, plural) - radix (exact) - 根 (Japanese, exact) - aerial root (narrow) - climbing root (narrow) - plant_anatomy - PO:0009005 - - - - - - - - - - Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). - root - - - - - - - - - A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. - - PO_GIT:135 - sistema de epiblasto (epiblastema) (Spanish, exact) - シュート系、苗条系 (Japanese, exact) - tree crown (narrow) - plant_anatomy - Poaceae crown (related) - shoot (related) - thalli (related) - thallus (related) - PO:0009006 - - - The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. - shoot system - - - - - - - - - A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. - - portion of tissue (broad) - tissue (broad) - PO_GIT:59 - porci&#243n de un tejido vegetal (Spanish, exact) - 植物組織の一部 (Japanese, exact) - plant_anatomy - plant tissue (related) - PO:0009007 - - - A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. - portion of plant tissue - - - - - - - - - A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. - - organ (broad) - PO_GIT:55 - &#243rgano vegetal (Spanish, exact) - 植物 器官 (Japanese, exact) - plant_anatomy - compound plant organ (related) - simple plant organ (related) - PO:0009008 - - Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). - plant organ - - - - - - - - - A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631). - - embryo (broad) - PO_GIT:92 - embri&#243n (Spanish, exact) - 植物胚 (Japanese, exact) - plant_anatomy - germ (related) - PO:0009009 - A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa; the beginning of a seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010). - plant embryo - - - - - - - - - - - - - - - - - - - - - A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088). - - diaspore (broad) - PO_GIT:405 - semilla (Spanish, exact) - 種子 (Japanese, exact) - pyrene (narrow) - plant_anatomy - PO:0009010 - - - - - - - - - - A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms). - seed - - - - - - - - - - A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. - - - PO_GIT:57 - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant_anatomy - PO:0009011 - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - plant structure - - - - - - - - - A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. - - PO:0007021 - PO_GIT:185 - etapa de desarrollo de estructura vegetal (Spanish, exact) - plant growth and development stage (exact) - plant_structure_development_stage - Arabidopsis growth (related) - PO:0009012 - - Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. - plant structure development stage - - - - - - - - - - - - - - - A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. - - PO_GIT:472 - meristem (exact) - meristema (Spanish, exact) - meristematic tissue (exact) - 分裂組織 (Japanese, exact) - plant_anatomy - PO:0009013 - - portion of meristem tissue - - - - - - - - - - - - - - - - - - - - - A leaf (PO:0025034) in a vascular plant. - - PO_GIT:137 - foliage leaf (exact) - hoja vascular (Spanish, exact) - leaf, vascular (exact) - vascular leaves (exact, plural) - 維管束のある葉, または維管束植物の葉 (Japanese, exact) - ascidia (narrow) - ascidium (narrow) - fiddlehead (narrow) - frond (narrow) - needle-like leaf (narrow) - pitcher (narrow) - pitcher blade (narrow) - pitcher-blade (narrow) - scale-like leaf (narrow) - sterile frond (narrow) - trophophyll (narrow) - plant_anatomy - crozier (related) - macrophyll (related) - megaphyll (related) - PO:0009025 - - - - - - - - - - - - - Has vascular tissue. From APweb Glossary: In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud. Occurs in the sporophytic phase of a plant life cycle. - vascular leaf - - - - - - - - - - - - - - - A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part. - - PO:0004541 - PO_GIT:160 - PO_GIT:259 - flor (Spanish, exact) - 花 (Japanese, exact) - Asteraceae floret (narrow) - basal flower (narrow) - double flower (narrow) - hermaphrodite flower (narrow) - monoclinous flower (narrow) - perfect flower (narrow) - plant_anatomy - floret (related) - PO:0009046 - - - - The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form. - flower - - - - - - - - - A shoot axis (PO:0025029) that is the primary axis of a plant. - - PO_GIT:52 - PO_GIT:96 - ca&#241a (Spanish, exact) - culm (exact) - eje primario (Spanish, exact) - primary axis (exact) - primary stem (exact) - tallo (Spanish, exact) - tronco (Spanish, exact) - 茎 (Japanese, exact) - bole (narrow) - cane (narrow) - caudex (narrow) - caudices (narrow) - core (narrow) - primocane (narrow) - scape (narrow) - stalk (narrow) - trunk (narrow) - plant_anatomy - PO:0009047 - - - A stem often bears leaves and buds. It is usually above ground, and is more or less negatively geotropic. - stem - - - - - - - - - - - - - - - - - - - - - A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046). - - PO:0006317 - PO:0006357 - PO:0006365 - PO:0006384 - PO:0006391 - PO:0006394 - PO:0006403 - PO:0006404 - PO:0006423 - PO:0006424 - PO:0006425 - PO:0006426 - PO:0025089 - pistil (broad) - PO_GIT:470 - PO_GIT:71 - PO_GIT:98 - ginoecio (Spanish, exact) - gynaecium (exact) - gynoecia (exact, plural) - 雌蕊群 (Japanese, exact) - Poaceae gynoecium (narrow) - Zea gynoecium (narrow) - apocarpous gynoecium (narrow) - gynoecium of ear floret (narrow) - gynoecium of lower floret of pedicellate spikelet of ear (narrow) - gynoecium of lower floret of pedicellate spikelet of tassel (narrow) - gynoecium of lower floret of sessile spikelet of ear (narrow) - gynoecium of lower floret of sessile spikelet of tassel (narrow) - gynoecium of tassel floret (narrow) - gynoecium of upper floret of pedicellate spikelet of ear (narrow) - gynoecium of upper floret of pedicellate spikelet of tassel (narrow) - gynoecium of upper floret of sessile spikelet of ear (narrow) - gynoecium of upper floret of sessile spikelet of tassel (narrow) - syncarpous gynoecium (narrow) - plant_anatomy - PO:0009062 - - - If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). - gynoecium - - - - - - - - - - - - - - - A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006). - - PO:0006457 - PO:0006491 - PO_GIT:464 - PO_GIT:70 - &#243vulo vegetal (Spanish, exact) - 胚珠 (Japanese, exact) - Poaceae ovule (narrow) - Zea ovule (narrow) - plant_anatomy - PO:0020003 - - - A seed (PO:0009010) develops from a plant ovule. In angiosperms, a plant ovule is part of a plant ovary (PO:0009072). In conifers, a plant ovule is part of an ovuliferous scale (add term). If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352). - plant ovule - - - - - - - - - An embryo root (PO:0000045) that is the basal continuation of a hypocotyl (PO:0020100) in a plant embryo (PO:0009009) or a seedling (PO:0000003). - - PO_GIT:344 - rad&#237cula (Spanish, exact) - 幼根 (Japanese, exact) - plant_anatomy - PO:0020031 - - May develop into the primary root (PO:0020127) and eventually the root system (PO:0025025) of an adult plant. Sometimes abortive. - radicle - - - - - - - - - - - - - - - A stalk (PO:0025066) of a vascular leaf (PO:0009025). - - http://www.langual.org/langual_thesaurus.asp?termid=C0304 - pec&#237olo (Spanish, exact) - 葉柄 (Japanese, exact) - plant_anatomy - PO:0020038 - - LanguaL definition: Leafstalk, the slender, usually cylindrical portion of a leaf, which supports the blade and is attached to the stem (Source: Webster's) - petiole - - - - - - - - - - - - - - - A root (PO:0009005) that develops directly from a seedling radicle (PO:0020127). - - PO:0020089 - PO_GIT:161 - ra&#237z primaria (Spanish, exact) - tap root (exact) - 一次根 (Japanese, exact) - plant_anatomy - PO:0020127 - - The first root of a plant. In dicots and gymnosperms it becomes the tap root, the central axis of a root system (PO:0025025). - primary root - - - - - - - - - - - - - - - A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). - - promeristem (broad) - PO_GIT:579 - AM (exact) - meristema apical (Spanish, exact) - 頂端分裂組織 (Japanese, exact) - plant_anatomy - primary meristem (related) - PO:0020144 - - apical meristem - - - - - - - - - - - - - - - - A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). - - promeristem (broad) - PO_GIT:472 - SAM (exact) - meristema apical del epiblasto (epiblastema) (Spanish, exact) - 茎頂分裂組織 (Japanese, exact) - plant_anatomy - primary shoot meristem (related) - PO:0020148 - - shoot apical meristem - - - - - - - - - - - - - - - - - - - - - - - - - - A cardinal part of multi-tissue plant structure (PO:0025498) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types. - - rwalls - 2010-02-11T01:18:24Z - PO_GIT:52 - PO_GIT:60 - cardinal part of plant organ (exact) - parte de un &#243rgano cardinal (Spanish, exact) - 基本的な（主要な）器官部 (Japanese, exact) - plant_anatomy - PO:0025001 - - - Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs. - cardinal organ part - - - - - - - - - An axial plant organ (PO:0009008). - - rwalls - 2010-07-01T03:44:41Z - eje de la planta (Spanish, exact) - plant axes (exact, plural) - 植物軸（軸柱） (Japanese, exact) - plant_anatomy - PO:0025004 - - Includes roots and shoots. - plant axis - - - - - - - - - - - - - - - A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). - - rwalls - 2010-02-09T04:12:11Z - PO_GIT:63 - estructura vegetal colectiva de &#243rgano (Spanish, exact) - 集合植物器官構造 (Japanese, exact) - plant_anatomy - PO:0025007 - - Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. - collective plant organ structure - - - - - - - - - A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005). - - Laurel_Cooper - 2010-04-28T11:04:34Z - PO:0008033 - cycle (broad) - verticil (broad) - PO_GIT:90 - PO_GIT:99 - estructura colectiva del filoma (Spanish, exact) - 葉的器官が集まった構造 (Japanese, exact) - floral whorl (narrow) - whorl (narrow) - plant_anatomy - phyllome whorl (related) - PO:0025023 - - collective phyllome structure - - - - - - - - - - - - - - - A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. - - rwalls - 2010-07-01T02:11:26Z - root (broad) - PO_GIT:136 - sistema de ra&#237z (Spanish, exact) - 根系 (Japanese, exact) - plant_anatomy - PO:0025025 - - Generally the below ground portion of a vascular plant. - root system - - - - - - - - - - - - - - - A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). - - rwalls - 2010-07-01T03:46:35Z - caullome (exact) - eje del epiblasto (epiblastema) (Spanish, exact) - シュート軸 (Japanese, exact) - plant_anatomy - shoot (related) - PO:0025029 - - - - - - - Often bears leaves and branches. In vascular plants, has at least one node and one internode. - shoot axis - - - - - - - - - - A phyllome (PO:0006001) that is not associated with a reproductive structure. - - http://langual.org - rwalls - 2010-07-12T01:31:44Z - PO_GIT:274 - PO_GIT:301 - http://www.langual.org/langual_thesaurus.asp?termid=C0200 - hoja (Spanish, exact) - 葉 (Japanese, exact) - plant_anatomy - PO:0025034 - - LanguaL definition: The flat or fleshy expanded blade (lamina) including a small and insignificant leafstalk but excluding a large and fleshy leafstalk such as celery stalks or rhubarb stalks. - -LanguaL curation note: If the part indexed consists of a large leafstalk and a leaf blade, use *PLANT ABOVE SURFACE, EXCLUDING FRUIT OR SEED*. Compare *STEM, STALK (WITHOUT LEAVES)*. - leaf - - - - - - - - - A cardinal organ part (PO:0025001) that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part. - - Laurel_Cooper - 2009-12-18T10:09:17Z - PATO:0001873 - PATO:0002226 - PO_GIT:52 - PO_GIT:78 - tallo de alto orden (secundario, terciario, etc) (Spanish, exact) - 柄 (Japanese, exact) - plant_anatomy - stipe (related) - PO:0025066 - - Some stalks may be ridged or grooved. - stalk - - - - - - - - - - - - - - - A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094). - - rwalls - 2010-09-17T09:49:10Z - sistema de brote reproductivo (Spanish, exact) - 生殖シュート 系、苗条系 (Japanese, exact) - plant_anatomy - PO:0025082 - - reproductive shoot system - - - - - - - - - - - - - - - - - - - - - - - - - - A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009). - - rwalls - 2010-11-05T01:36:24Z - PO_GIT:245 - PO_GIT:339 - embryonic plant structure (exact) - estructura vegetal embri&#243nica (Spanish, exact) - 胚性植物構造 (Japanese, exact) - plant_anatomy - PO:0025099 - Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle). - embryo plant structure - - - - - - - - - A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). - - rwalls - 2010-11-15T09:10:22Z - PO_GIT:186 - portion of primordial tissue (exact) - portion of primordium tissue (exact) - primordia (exact, plural) - primordio (Spanish, exact) - 原基（可視的） (Japanese, exact) - plant_anatomy - PO:0025127 - A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. - primordium - - - - - - - - - - - - - - - - - - - - - A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001). - - rwalls - 2010-11-15T09:27:11Z - PO_GIT:466 - phyllome primordia (exact, plural) - portion of phyllome primordium tissue (exact) - primordio del filoma (Spanish, exact) - フィロム原基（可視的） (Japanese, exact) - plant_anatomy - PO:0025128 - The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop. - phyllome primordium - - - - - - - - - An anatomical entity that is or was part of a plant. - - rwalls - 2010-11-15T11:41:38Z - PO_GIT:224 - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant_anatomy - PO:0025131 - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - plant anatomical entity - - - - - - - - - A shoot apex that has as part a reproductive shoot apical meristem. - - rwalls - 2010-12-20T08:47:03Z - &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0025222 - reproductive shoot apex - - - - - - - - - - - - - - - A shoot apex PO:0000037) that has as part a vegetative shoot apical meristem (PO:0008016). - - rwalls - 2010-12-20T08:47:03Z - PO_GIT:234 - &#225pice vegetativo del epiblasto (epiblastema) (Spanish, exact) - 栄養シュート頂、栄養枝頂 (Japanese, exact) - plant_anatomy - PO:0025223 - vegetative shoot apex - - - - - - - - - - - - - - - - - - - - - A portion of plant tissue (PO:0009007) that is part of a plant embryo (PO:0009009). - - rwalls - 2010-12-20T12:27:10Z - portion of embryo tissue (broad) - PO_GIT:338 - portion of embryonic plant tissue (exact) - tejido embri&#243nico vegetal (Spanish, exact) - 植物胚性組織 の一部 (Japanese, exact) - plant_anatomy - PO:0025233 - This class is for tissues that only occur as part of an embryo. - portion of embryo plant tissue - - - - - - - - - - A radicle (PO:0020031) that is part of a plant embryo (PO:0009009). - - rwalls - 2011-04-25T10:41:14Z - PO_GIT:344 - embryonic radicle (exact) - rad&#237cula del embri&#243n (Spanish, exact) - 胚幼根 (Japanese, exact) - plant_anatomy - PO:0025296 - - May eventually develop into the root system (PO:0025025) of an adult plant. Sometimes is abortive. - plant embryo radicle - - - - - - - - - - - - - - - A radicle (PO:0020031) that is part of a whole plant (PO:0000003) in the seedling development stage (PO:0007131). - - rwalls - 2011-04-25T10:41:48Z - PO_GIT:344 - rad&#237cula de la pl&#225ntula (Spanish, exact) - 実生幼根 (Japanese, exact) - plant_anatomy - PO:0025297 - Develops from an embryo radicle (PO:0025296). May develop into the root system (PO:0025025) of an adult plant. Sometimes is abortive. - seedling radicle - - - - - - - - - A maximal whole plant development stage. - - rwalls - 2011-10-19T10:54:37Z - PO_GIT:230 - vida de la planta entera (Spanish, exact) - 植物体の一生 (Japanese, exact) - plant_structure_development_stage - PO:0025337 - There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. - life of whole plant stage - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497). - - rwalls - 2011-10-19T11:12:49Z - PO_GIT:391 - etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact) - 集合的植物構造の発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0025338 - Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). - collective plant organ structure development stage - - - - - - - - - A short, enlarged shoot system (PO:0009006) that has as parts a short stem (PO:0009047) in which the shoot internodes (PO:0005005) do not elongate, and one or more buds (PO:0000055) enclosed by fleshy leaves (PO:0009025) or leaf bases (PO:0020040). - - rwalls - 2011-11-16T03:39:15Z - diaspore (broad) - PO_GIT:173 - bulbo (Spanish, exact) - 球根、鱗茎 (Japanese, exact) - bulblet (narrow) - plant_anatomy - PO:0025356 - May serve as a storage and/or perennating organ. Usually underground. A bulb differs from a corm (PO:0025355) by having fleshy leaves or leaf bases. The outer leaves of a bulb are often dry and membranous, rather than fleshy. May bear adventitious roots. Examples include Alium and Tulipa. Not the same structure as a bulbil. - bulb - - - - - - - - - - - - - - - - - - - - - - - - - - A plant organ (PO:0009008) that is part of a flower (PO:0009046). - - rwalls - 2012-01-19T11:44:36Z - PO_GIT:423 - &#243rgano floral (Spanish, exact) - flower organ (exact) - 花器官 (Japanese, exact) - plant_anatomy - PO:0025395 - Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores. - floral organ - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) that is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148) and will give rise to a phyllome primordium (PO:0025128). - - Laurel_Cooper - 2012-02-07T08:20:10Z - phyllome meristem (broad) - PO_GIT:427 - フィロム原基 (Japanese, exact) - plant_anatomy - PO:0025430 - The phyllome anlagen is only detectable by gene expression, not morphology. - phyllome anlagen - - - - - - - - - - - - - - - A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a shoot apical meristem (PO:0020148). - - Laurel_Cooper - 2012-02-07T08:40:37Z - leaf meristem (broad) - PO_GIT:407 - 維管束系葉原基 (Japanese, exact) - plant_anatomy - PO:0025431 - This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied). - vascular leaf anlagen - - - - - - - - - A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). - - Laurel_Cooper - 2012-02-08T01:00:56Z - PO_GIT:427 - precursor de ra&#237 (Spanish, exact) - 根原基 (Japanese, exact) - plant_anatomy - PO:0025433 - Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). - root anlagen - - - - - - - - - - - - - - - A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222). - - rwalls - 2012-04-26T03:57:09Z - PO_GIT:465 - floral structure primordia (exact, plural) - portion of floral structure primordium tissue (exact) - primordio de organo floral (Spanish, exact) - 花器官原基 (Japanese, exact) - plant_anatomy - PO:0025477 - - If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089). - floral organ primordium - - - - - - - - - A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. - - Laurel_Cooper - 2012-06-11T14:57:00Z - PO_GIT:480 - estructura vegetal con m&#250ltiples tejidos (Spanish, exact) - 複数の組織からなる植物構造 (Japanese, exact) - plant_anatomy - PO:0025496 - Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. - multi-tissue plant structure - - - - - - - - - A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). - - Laurel_Cooper - 2012-06-11T15:09:20Z - PO_GIT:479 - estructura vegetal colectiva (Spanish, exact) - 集合的植物構造 (Japanese, exact) - plant_anatomy - PO:0025497 - This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). - collective plant structure - - - - - - - - - - - - - - - A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types. - - Laurel_Cooper - 2012-06-11T15:28:44Z - PO_GIT:485 - parte cardinal de estructura vegetal con m&#250ltiples tejidos (Spanish, exact) - 複数の組織からなる植物構造の基本（主要）部分 (Japanese, exact) - plant_anatomy - PO:0025498 - Includes cardinal parts of plant organs (PO:0025001) as well as parts of other multi-tissue plant structures. Cardinal refers to the fact that these are biologically meaningful and not arbitrary parts. Most cardinal parts of multi-tissue plant structures have both fiat and bona-fide boundaries, including parts with large fiat boundaries, such as leaf base (PO:0020040) or fruit distal end (PO:0008001), and parts with primarily bona-fide boundaries, such as leaflet (PO:0020049). - cardinal part of multi-tissue plant structure - - - - - - - - - A plant axis (PO:0025004) that is radially enlarged. - - Laurel_Cooper - 2012-11-20T18:35:45Z - PO_GIT:127 - 塊茎 (Japanese, exact) - plant_anatomy - PO:0025522 - - Functions in storage of photosynthate metabolites. May develop from a branch (PO:0025073) or a root (PO:0009005). If you are annotating to tuber, you should pick the more specific child term: shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476). - tuber - - - - - - - - - - - - - - - A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death. - - Laurel_Cooper - 2012-12-13T18:21:19Z - PO_GIT:517 - plant_structure_development_stage - PO:0025527 - The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003). - shoot system development stage - - - - - - - - - A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082). - - Laurel_Cooper - 2012-12-13T19:01:14Z - PO_GIT:517 - plant_structure_development_stage - PO:0025530 - reproductive shoot system development stage - - - - - - - - - A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). - - Laurel_Cooper - 2014-05-13T16:51:47Z - PO_GIT:586 - plant_anatomy - PO:0025606 - A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). - native plant cell - - - - - - - - - - - - - - - A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. - - rwalls - 2010-07-15T02:56:11Z - PO_GIT:139 - PO_GIT:68 - fase esporof&#237tica (Spanish, exact) - sporophytic development stage (exact) - sporophytic phase (exact) - sporphyte phase (exact) - 胞子体発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0028002 - - A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. - sporophyte development stage - - - - - - - - - A fruit (PO:0009001) which develops from a carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and a stony endocarp (PO:0009086). - - indehiscent fruit (broad) - PO_GIT:647 - drupa (exact, Spanish) - drupe (exact) - steinfrucht (exact, German) - stone fruit (exact) - whole pit fruit - plant_anatomy - PO:0030103 - May develop from an inferior or superior carpel (PO:0009030) and may contain one or more seeds (PO:0009010). Examples: Amborella trichopoda (basal angiosperm), coffee (Coffea canephora), Cornaceae (Davidia spp.), cashew (Anacardium occidentale), coconut (Cocos nucifera), and almond, peach and plum (Prunus spp.). - drupe fruit - - - - - - - - - A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085). - - indehiscent fruit (broad) - PO_GIT:652 - bacca (exact) - baya (exact, Spanish) - beere (exact, German) - berry (exact) - pyrine (narrow) - plant_anatomy - PO:0030108 - Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera). - berry fruit - - - - - - - - - A berry fruit (PO:0030108) which develops from a superior gynoecium (PO:0009062) and at maturity comprises a thickened exocarp (PO:0009085), thickened mesocarp (PO:0009087), and endocarp (PO:0009086), and has as parts juice sacs (PO:0006013) on a carpel adaxial epidermis (PO:0025618). - - indehiscent fruit (broad) - panzerbeere (broad, German) - PO_GIT:652 - citrus fruit (exact) - hesperide (exact, German) - hesperidio (exact, Spanish) - hesperidium (exact) - plant_anatomy - PO:0030109 - A hesperidium fruit (PO:0030109) develops from a superior gynoecium (PO:0009062), and therefore is not surrounded by receptacle (PO:0009064) tissue. Examples: orange, grapefruit, lemon, and lime (Citrus spp.). - hesperidium fruit - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit (PO:0030108) which develops from an inferior gynoecium (PO:0009062) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and hardened endocarp (PO:0009086) and has as a part a fleshy hypanthium (PO:0009065) which is indistinct from the exocarp (PO:0009085). - - indehiscent fruit (broad) - PO_GIT:652 - apfelfrucht (exact, German) - kernfrucht (exact, German) - kernobst (exact, German) - pome (exact) - pomo (exact, Spanish) - plant_anatomy - PO:0030110 - A pome fruit (PO:0030110) is a specialized type of berry fruit (PO:0030108) which is encapsuled in persistent, accrescent receptacle (PO:0009064) and/or hypanthium (PO:0009065) tissue. Examples: Apple, crab apple, and pear (Malus spp. and Pyrus spp.) - pome fruit - - - - - - - - - A berry fruit (PO:0030108) which develops from an inferior carpel (PO:0009030) and at maturity comprises a fleshy exocarp (PO:0009085), fleshy mesocarp (PO:0009087), and fleshy endocarp (PO:0009086), and has as a part a hard receptacle (PO:0009064) which surrounds, and is indistinct from, the exocarp (PO:0009085). - - indehiscent fruit (broad) - panzerbeere (broad, German) (broad) - PO_GIT:652 - kürbisfrucht (exact, German) - pepo (exact) - pepónide (exact, Spanish) - plant_anatomy - PO:0030111 - A pepo fruit (PO:0030111) is specialized type of berry fruit (PO:0030108) which is encapsuled by persistent, accrescent receptacle (PO:0009064) tissue. The rind, or tough outer covering, of pepo fruits comprises receptical tissue and at least the exocarp (PO:0009085) layer of the pericarp (PO:0009084). Examples: pumpkin (Cucurbita pepo), cucumber (Cucumis sativus), and watermelon (Citrullus lanatus) and banana (Musa acuminata). - pepo fruit - - - - - - - - - - - - - - - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - - multi-cellular organism - multicellular organism - - - - - - - - - A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. - - glandula mammaria - lactiferous gland - mammary gland - - - - - - - - - - - - - - - - An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0235 - mammal milk - mammary gland milk - LanguaL curation note: See scope note for *MILK OR MILK COMPONENT*. for lowfat milk use *FAT PARTIALLY REMOVED*; for skim milk, use *FAT FULLY REMOVED* (both found in D3. TREATMENT APPLIED). - milk - - - - - - - - - Gonochoristic organism that can produce female gametes. - - female organism - - - - - - - - - - - - - - - - - - - A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO]. - egg shell - - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=C0278 - egg shell - shell (egg) - LanguaL term definition: The covering of a bird or reptile egg. - eggshell - - - - - - - - - Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - - fluid - body fluid - bodily fluid - - - - - - - - - A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. - - adults - adult organism - - - - - - - - - - - - - - - - - - The yellow spheroidal mass of stored food that forms the inner portion of the egg of a bird or reptile and is surrounded by the white. - egg yolk - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0215 - egg yolk - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - egg (with shell) - The hard-shelled reproductive body produced by a bird (especially by the common domestic chicken) or a reptile; also: its contents used as food. - whole egg in shell - - http://langual.org - Note that this is cross referenced to both LanguaL "egg" as well as "whole egg in shell" - http://www.langual.org/langual_thesaurus.asp?termid=C0128 - http://www.langual.org/langual_thesaurus.asp?termid=C0274 - LanguaL curation note: The egg shell functions as a container. Therefore, the physical state of a raw egg in the shell is *LIQUID, HIGH VISCOSITY, WITH NO VISIBLE PARTICLES*. - shelled egg - - - - - - - - - - - - - - - - - - Albumen is the clear liquid contained within an egg and consists of water and proteins, among which are ovomucin and ovomucoid. It protects the egg yolk and provides additional nutrition for the growth of the embryo. - egg white, albumen - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0241 - egg white - egg white - albumen - - - - - - - - - - unit - - - - - - - - - - length unit - - - - - - - - - - mass unit - - - - - - - - - - base unit - - - - - - - - - - volume unit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoon - tablespoons - - - - - - - - - - inch based unit - - - - - - - - - - quart based unit - - - - - - - - - - ounce based unit - - - - - - - - - - pound based unit - - - - - - - - - - teaspoon based unit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - a - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - juice - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - paste - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - cups - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <not applicable> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - half - - - - - - - - - - - - - - - - - in the pot - - - - - - - - - - - - - - - - - Puréed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Juice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - paste - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoons - - - - - - - - - - - - - - - - - hot, shimmering - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - a - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - juice - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - paste - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cups - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - <not applicable> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - half - - - - - - - - - - - - - - - - - in the pot - - - - - - - - - - - - - - - - - Puréed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Juice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - paste - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoons - - - - - - - - - - - - - - - - - hot, shimmering - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A tasty red lentil soup. - - - Red Lentil Soup - - - - - - - - - - - - - - - - - - - - - - - - - - - - 80 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 80 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 80 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - juice - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - halved - - - - - - - - - - - - - - - - - - - - 6 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - wedges - - - - - - - - - - - - - - - - - Juice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - wedges - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - wedges - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - half - - - - - - - - - - - - - - - - - leaves - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plumped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 80 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 80 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 80 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - juice - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - halved - - - - - - - - - - - - - - - - - - - - - - 6 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - wedges - - - - - - - - - - - - - - - - - Juice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - wedges - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - wedges - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - half - - - - - - - - - - - - - - - - - leaves - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - plumped - - - - - - - - - - - - - - - A crisp and flavorful salad which combines apples, walnuts, celery, raisins, mayonnaise and sugar - - - Waldorf Salad - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2023-03-21T23:26:58Z - AnimalProductRecipe - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2023-03-21T23:26:58Z - MeatRecipe - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2023-03-21T23:26:58Z - RecipeContainingMilk - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2023-03-21T23:26:58Z - RecipeContainingWheat - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - incorporated - - - - - - - - - - - - - - - - - beaten - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - Boiled - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chilled - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - smooth and firm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cut - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - incorporated - - - - - - - - - - - - - - - - - beaten - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - Boiled - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chilled - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - smooth and firm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cut - - - - - - - - - - - - - - - Homemade egg noodles that are boiled until tender for use in your favorite recipe. - - - Homemade Egg Noodles - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - 1 1⁄2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - uncooked - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - done - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - peppered - - - - - - - - - - - - - - - - - flavoured - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - 1 1⁄2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - uncooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - done - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - peppered - - - - - - - - - - - - - - - - - flavoured - - - - - - - - - - - - - - - - - - - - - - - - A recipe for a simple spaghetti featuring sautéed onions, bell peppers and hamburger meat. - - - Simple Spaghetti - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 3-4 - - - - - - - - - - - - - - - - - poached - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 14.5 - - - - - - - - - - - - - - - - - creamed - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - small - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - cloves - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - shredded (cheddar, mozzarella, Mexican blend) - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - meat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pre-cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3-4 - - - - - - - - - - - - - - - - - poached - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 14.5 - - - - - - - - - - - - - - - - - creamed - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - small - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - cloves - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - shredded (cheddar, mozzarella, Mexican blend) - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - meat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pre-cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This is a traditional Mexican soup that can be made with a rotisserie chicken or poached chicken. It is full of flavor and garnished with cilantro, lime juice, sour cream, cheese, avocado, and corn chips. - - - Tortilla Soup - - - - - - - - - - - - - - - - - - - - - - - - - - - - beaten - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - medium-high - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - no longer pink in the center - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped/Diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - beaten - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - medium-high - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - no longer pink in the center - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped/Diced - - - - - - - - - - - - - - - Patties are made of ground turkey, spinach, feta, eggs and garlic and grilled until no longer pink in the center. - - - Spinach and Feta Turkey Burgers - - - - - - - - - - - - - - - - - - - - - - - - - - - - to taste - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - fresh spears - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - olive oil - - - - - - - - - - - - - - - - - spears - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - high heat, oil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to taste - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - fresh spears - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - olive oil - - - - - - - - - - - - - - - - - spears - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - high heat, oil - - - - - - - - - - - - - - - - - - - - - - - - A delicious and easy side dish of grilled asparagus. - - - Grilled Asparagus - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - bite-size - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 12 - - - - - - - - - - - - - - - - - dry - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.125 - - - - - - - - - - - - - - - - - Crushed - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 tablespoons - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - browned - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - heated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - 1/2 teaspoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3/4 cup - - - - - - - - - - - - - - - - - 3 tablespoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - drained - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to - - - - - - - - - - - - - - - - - thickens - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lightly salted water - - - - - - - - - - - - - - - - - boil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - heated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - stirred - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - boil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - whisked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - bite-size - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 12 - - - - - - - - - - - - - - - - - dry - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.125 - - - - - - - - - - - - - - - - - Crushed - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 tablespoons - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - browned - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - heated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - 1/2 teaspoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3/4 cup - - - - - - - - - - - - - - - - - 3 tablespoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - drained - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to - - - - - - - - - - - - - - - - - thickens - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lightly salted water - - - - - - - - - - - - - - - - - boil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - heated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - stirred - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - boil - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - whisked - - - - - - - - - - - - - - - This stir-fry combines noodles with pork, vegetables, and a flavorful sauce to create a delicious meal. - - - - - - Sweet and Spicy Pork and Napa Cabbage Stir-Fry with Spicy Noodles - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped raw - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - Shredded - - - - - - - - - - - - - - - - - - - - - - - - - - 1.5 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1.5 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - uncooked - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - drippings - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - drippings - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - 2 tablespoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - medium heat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cup - - - - - - - - - - - - - - - - - melted - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Hot drippings - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - bright pink - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.75 - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped raw - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - Shredded - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1.5 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1.5 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - uncooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - drippings - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - drippings - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - 2 tablespoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - medium heat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cup - - - - - - - - - - - - - - - - - melted - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Hot drippings - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - bright pink - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A savory grits dish featuring shrimp, cheese, bacon and vegetables. - - - - - Shrimp and Cheesy Grits with Bacon - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - whole - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 1/2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - extracted - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - - - - - - - - - remaining - - - - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - preheated - - - - - - - - - - - - - - - - - - - - - - - - - - - extracted - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - slice - - - - - - - - - - - - - - - - - coated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - slice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - remaining - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - brown - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - whole - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 4 1/2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.5 - - - - - - - - - - - - - - - - - extracted - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - - - - - - - - - - - remaining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ________ - - - - - - - - - - - - - - - - - preheated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - extracted - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - slice - - - - - - - - - - - - - - - - - coated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - slice - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - remaining - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - brown - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A recipe featuring egg-soaked brioche waffles - - - - Easy French Toast Waffles - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - cubed - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - fresh - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - cloves - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - until heated through - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pureed - - - - - - - - - - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - slightly tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lightly browned - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - smooth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - cubed - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - fresh - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - cloves - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - until heated through - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - pureed - - - - - - - - - - - - - - - - - - - - - - - - - - none - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - slightly tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - lightly browned - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tablespoon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - smooth - - - - - - - - - - - - - - - A spicy Indian dish composed of spinach pureed with onion, garlic, and tomato, and cooked together with paneer. - - - Easy Palak Paneer - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - - - - - - - - - - 0.33333334326744 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - thinly sliced - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cloves - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - rest - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - well blended - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - about a tablespoon of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - deglazed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - meat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.33333334326744 - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - thinly sliced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - cooked - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cloves - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - rest - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sliced - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - broth - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - well blended - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - about a tablespoon of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - deglazed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - N/A - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - meat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Spicy Thai Basil Chicken (Pad Krapow Gai) served with hot cooked rice. - - - Spicy Thai Basil Chicken (Pad Krapow Gai) - - - - - - - - - - - - - - - - - - - - - - - - - - - - to taste - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - Crushed - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Wilted - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ribs - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - leaves - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to taste - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 0.25 - - - - - - - - - - - - - - - - - Crushed - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - minced - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Wilted - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ribs - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - leaves - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A sauteed dish made of Lacinato kale spiced up with red pepper flakes, garlic, and red wine vinegar. - - - - Sauteed Lacinato Kale - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - vinegar - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - root - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - blended - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to a bowl - - - - - - - - - - - - - - - - - Refrigerated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - a boil - - - - - - - - - - - over high heat - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - vinegar - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - root - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - blended - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to a bowl - - - - - - - - - - - - - - - - - Refrigerated - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - a boil - - - - - - - - - - - over high heat - - - - - - - - - A spicy sauce made with water, rice vinegar, sugar, ginger root, chile pepper, ketchup, and garlic. - - - Sweet Chili Thai Sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6 - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - ¼ - - - - - - - - - - - - - - - - - blanched - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - clove - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - - - - - - - - - - - - 1½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - ¾ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - for serving - - - - - - - - - - - - - - - toasted - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - - zest - - - - - - - - - - - - - - - - - Remaining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Tbsp. - - - - - - - - - - - - - - - - - - - - - - - - - - brown - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tossed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Tbsp. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - Tbsp. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sprigs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ricotta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - reserved - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 6 - - - - - - - - - - - - - - - - - n/a - - - - - - - - - - - - - - - - - - - - - - - - - - - - ¼ - - - - - - - - - - - - - - - - - blanched - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - clove - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - crushed - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - ¾ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - for serving - - - - - - - - - - - - - - - toasted - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - ground - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - zest - - - - - - - - - - - - - - - - - Remaining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Tbsp. - - - - - - - - - - - - - - - - - - - - - - - - - - brown - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tossed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Tbsp. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - flakes - - - - - - - - - - - - - - - - - Tbsp. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - sprigs - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ricotta - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - reserved - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Roasted hazelnuts, mint, garlic, white wine vinegar, crushed red pepper flakes and ricotta combined with summer squash for a flavorful, savory dish. - - - - Marinated Zucchini With Hazelnuts and Ricotta - - - - - - - - - - - - - - - - - - - - - - - - - - - - ¼ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - ⅛ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - large - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - bag - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - halved - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - smooth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mashed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ¼ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - ⅛ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - large - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - bag - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - halved - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - smooth - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mashed - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A recipe for classic deviled eggs with mayonnaise, dijon mustard, cayenne pepper and garnishes of paprika and chives. - - - Classic Deviled Eggs - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - thinly - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 ½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - be made 2 weeks ahead - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 ingredients - - - - - - - - - - - - - - - - - water - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - thinly - - - - - - - - - - - - - - - - - Chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 ½ - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - mixture - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - be made 2 weeks ahead - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - temperature - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 3 ingredients - - - - - - - - - - - - - - - - - water - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - - - dissolved - - - - - - - - - - - - - - - A recipe for quick-pickled red onions involving whisking of apple cider vinegar, sugar and salt, adding onions to a jar, and letting sit for one hour. - - - - Quick-Pickled Red Onions - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - whole - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - Fried - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - dried - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1/4 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - whole - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - Fried - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - dried - - - - - - - - - - - - - - - A guide to making corn dogs at home by combining various ingredients and following a series of steps. - - - - How To Make Easy Homemade Corn Dogs - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Breakfast - - - Brunch - - - Gluten-Free - - - Grilling - - - Main - - - Recipe - - - Seafood - - - Snacks - - - Stir-Fry - - - Vegetarian - - - Main Course - - - Main Dish - - - Main dish - - - Side Dish - - - - inch - - - - quart - quarts - - - - ounce - ounces - - - - pound - pounds - - - - teaspoon - teaspoons - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/output/reaction-20657015.pickle b/tests/output/reaction-20657015.pickle deleted file mode 100644 index 4df38ebcc..000000000 Binary files a/tests/output/reaction-20657015.pickle and /dev/null differ diff --git a/tests/output/reaction-20657015.yaml b/tests/output/reaction-20657015.yaml deleted file mode 100644 index 328478c23..000000000 --- a/tests/output/reaction-20657015.yaml +++ /dev/null @@ -1,105 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/reaction-20657015.txt -input_text: "Title: Molecular identification of N-acetylaspartylglutamate synthase\ - \ and beta-citrylglutamate synthase\n\nAbstract\nThe purpose of the present work\ - \ was to determine the identity of the enzymes that synthesize N-acetylaspartylglutamate\ - \ (NAAG), the most abundant dipeptide present in vertebrate central nervous system\ - \ (CNS), and \u03B2-citrylglutamate, a structural analogue of NAAG present in testis\ - \ and immature brain. Previous evidence suggests that NAAG is not synthesized on\ - \ ribosomes but presumably is synthesized by a ligase. As attempts to detect this\ - \ ligase in brain extracts failed, we searched the mammalian genomes for putative\ - \ enzymes that could catalyze this type of reaction. Mammalian genomes were found\ - \ to encode two putative ligases homologous to Escherichia coli RIMK, which ligates\ - \ glutamates to the C terminus of ribosomal protein S6. One of them, named RIMKLA,\ - \ is almost exclusively expressed in the CNS, whereas RIMKLB, which shares 65% sequence\ - \ identity with RIMKLA, is expressed in CNS and testis. Both proteins were expressed\ - \ in bacteria or HEK293T cells and purified. RIMKLA catalyzed the ATP-dependent\ - \ synthesis of N-acetylaspartylglutamate from N-acetylaspartate and l-glutamate.\ - \ RIMKLB catalyzed this reaction as well as the synthesis of \u03B2-citrylglutamate.\ - \ The nature of the reaction products was confirmed by mass spectrometry and NMR.\ - \ RIMKLA was shown to produce stoichiometric amounts of NAAG and ADP, in agreement\ - \ with its belonging to the ATP-grasp family of ligases. The molecular identification\ - \ of these two enzymes will facilitate progress in the understanding of the function\ - \ of NAAG and \u03B2-citrylglutamate." -raw_completion_output: "genes: RIMKLB; RIMKLA;\nreactions: N-acetylaspartate + l-glutamate\ - \ = N-acetylaspartylglutamate + ADP; N-acetylaspartate + l-glutamate = beta-citrylglutamate;\ - \ \ngene_reaction_pairings: RIMKLB: N-acetylaspartate + l-glutamate = N-acetylaspartylglutamate\ - \ + ADP; RIMKLB: N-acetylaspartate + l-glutamate = beta-citrylglutamate; RIMKLA:\ - \ N-acetylaspartate + l-glutamate = N-acetylaspartylglutamate + ADP; \norganism:\ - \ mammalian" -prompt: 'From the text below, extract the following entities in the following format: - - - gene: - - reaction: - - - - Text: - - RIMKLA: N-acetylaspartate + l-glutamate = N-acetylaspartylglutamate + ADP - - - === - - - ' -extracted_object: - genes: - - HGNC:29228 - - HGNC:28725 - reactions: - - label: N-acetylaspartate + l-glutamate reaction - description: A chemical reaction between N-acetylaspartate and l-glutamate, resulting - in the production of N-acetylaspartylglutamate and ADP - synonyms: - - NA - subclass_of: AUTO:Chemical%20Reaction - left_side: - - AUTO:N-acetylaspartate - - CHEBI:29988 - right_side: - - CHEBI:76931 - - CHEBI:16761 - - label: N-acetylaspartate synthesis - description: A reaction in which N-acetylaspartate is converted to beta-citrylglutamate - synonyms: - - N-acetylaspartic acid synthesis - - NAA synthesis - subclass_of: GO:0009058 - left_side: - - AUTO:N-acetylaspartate - - CHEBI:29988 - right_side: - - CHEBI:76942 - gene_reaction_pairings: - - gene: HGNC:29228 - reaction: AUTO:N-acetylaspartate%20%2B%20l-glutamate%20%3D%20N-acetylaspartylglutamate%20%2B%20ADP - - gene: HGNC:29228 - reaction: AUTO:N-acetylaspartate%20%2B%20l-glutamate%20%3D%20beta-citrylglutamate - - gene: HGNC:28725 - reaction: AUTO:N-acetylaspartate%20%2B%20l-glutamate%20%3D%20N-acetylaspartylglutamate%20%2B%20ADP - organism: AUTO:mammalian -named_entities: -- id: HGNC:29228 - label: RIMKLB -- id: HGNC:28725 - label: RIMKLA -- id: CHEBI:29988 - label: l-glutamate -- id: CHEBI:76931 - label: N-acetylaspartylglutamate -- id: CHEBI:16761 - label: ADP -- id: GO:0009058 - label: Anabolism -- id: CHEBI:29988 - label: l-glutamate -- id: CHEBI:76942 - label: beta-citrylglutamate -- id: HGNC:29228 - label: RIMKLB -- id: HGNC:29228 - label: RIMKLB -- id: HGNC:28725 - label: RIMKLA diff --git a/tests/output/reaction-21290071.pickle b/tests/output/reaction-21290071.pickle deleted file mode 100644 index 9d02f2e9a..000000000 Binary files a/tests/output/reaction-21290071.pickle and /dev/null differ diff --git a/tests/output/reaction-21290071.yaml b/tests/output/reaction-21290071.yaml deleted file mode 100644 index 27cafa1cf..000000000 --- a/tests/output/reaction-21290071.yaml +++ /dev/null @@ -1,114 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/reaction-21290071.txt -input_text: 'Title: Substrate specificity of Rv3378c, an enzyme from Mycobacterium - - tuberculosis, and the inhibitory activity of the bicyclic diterpenoids - - against macrophage phagocytosis - - - Abstract - - The Rv3378c gene product from Mycobacterium tuberculosis encodes a diterpene synthase - to produce tuberculosinol (3), 13R-isotuberculosinol (4a), and 13S-isotuberculosinol - (4b) from tuberculosinyl diphosphate (2). The product distribution ratios are 1 - : 1 for 3 to 4 and 1 : 3 for 4a to 4b. The substrate specificity of the Rv3378c-encoded - enzyme was examined. The 3 labdadienyl diphosphates, copalyl diphosphate (CDP) (7), - ent-CDP (8), and syn-CDP (9), underwent the conversion reaction, with good yields - (67-78%). Copalol (23) and manool (24) were produced from 7, ent-copalol (25) and - ent-manool (26) from 8, and syn-copalol (27) and vitexifolin A (28) from 9. The - ratio of 23 to 24 was 40 : 27, that of 25:26 was 22 : 50, and that of 27:28 was - 16 : 62. Analysis on a GC-MS chromatograph equipped with a chiral column revealed - that 24, 26, and 28 consisted of a mixture of 13R- (a) and 13S-stereoisomers (b) - in the following ratio: ca. 1 : 1 for 24a to 24b, ca. 1 : 5 for 26a to 26b, and - ca. 1 : 19 for 28a to 28b. The structures of these products indicate that the reactions - of the 3 CDPs proceeded in the same fashion as that of 2. This is the first report - on the enzymatic synthesis of natural diterpenes manool, ent-manool, and vitexifolin - A. Both Rv3377c and Rv3378c genes are found in virulent Mycobacterium species, but - not in avirulent species. We found that 3 and 4 inhibited the phagocytosis of opsonized - zymosan particles by human macrophage-like cells. Interestingly, the inhibitory - activity was synergistically increased by the coexistence of 3 and 4b. Other labdane-related - diterpenes, 13-16 and 23-28, had little or no inhibitory activity. This synergistic - inhibition by 3 and 4 may provide further advantage to the impairment of phagocyte - function, which might contribute to pathogenicity of M. tuberculosis. - - ' -raw_completion_output: ' - - Gene: Rv3378c - - Reactions: 2 -> 3 + 4; 7 -> 23 + 24; 8 -> 25 + 26; 9 -> 27 + 28 - - Organism: Mycobacterium tuberculosis' -prompt: 'Split the following piece of text into fields in the following format: - - - label: - - description: - - synonyms: - - subclass_of: - - left_side: - - right_side: - - - - Text: - - 9 -> 27 + 28 - - - === - - - ' -extracted_object: - gene: AUTO:Rv3378c - reactions: - - label: 2 to 3 + 4 - description: A reaction involving the transfer of 2 atoms to yield 3 and 4 atoms. - synonyms: - - None - subclass_of: AUTO:Reaction - left_side: - - AUTO:2 - right_side: - - AUTO:3 - - AUTO:4 - - label: reaction_7-23+24 - description: Reaction between 7 and 23, resulting in the production of 24 - synonyms: - - N/A - subclass_of: AUTO:Chemical%20Reaction - left_side: - - AUTO:7 - right_side: - - AUTO:23 - - AUTO:24 - - label: 8 to 25 and 26 - description: Chemical reaction that involves conversion of 8 to 25 and 26. - synonyms: - - n/a - subclass_of: AUTO:Conversion%20reaction - left_side: - - AUTO:8 - right_side: - - AUTO:25 - - AUTO:26 - - label: 9 to 27 and 28 reaction - description: A reaction in which 9 combines to form both 27 and 28 - synonyms: - - N/A - subclass_of: AUTO:Combination%20reaction - left_side: - - AUTO:9 - right_side: - - AUTO:27 - - AUTO:28 - organism: NCBITaxon:1773 -named_entities: -- id: MESH:D009169 - label: Mycobacterium tuberculosis diff --git a/tests/output/recipe-egg-noodles.pickle b/tests/output/recipe-egg-noodles.pickle deleted file mode 100644 index ef1d26ffc..000000000 Binary files a/tests/output/recipe-egg-noodles.pickle and /dev/null differ diff --git a/tests/output/recipe-egg-noodles.yaml b/tests/output/recipe-egg-noodles.yaml deleted file mode 100644 index e21717354..000000000 --- a/tests/output/recipe-egg-noodles.yaml +++ /dev/null @@ -1,354 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-egg-noodles.txt -input_text: "Homemade Egg Noodles\n\nGather the ingredients.\n\nCombine the flour\ - \ and salt in a large shallow bowl or on a clean work surface. Make a well in the\ - \ center, almost like a \"bowl\" of flour, to hold the eggs. Crack the eggs into\ - \ it.\n\nFlour with eggs cracked into the well in the center\nUse a fork to beat\ - \ the eggs and then gradually start incorporating the flour into the eggs. As you\ - \ beat them, they will slowly but surely take up some flour from the edges.\n\n\ - Eggs beat with a fork in a well in the center of flour\nKeep stirring and pulling\ - \ in more flour until a solid dough forms. The dough will be sticky. Don't worry;\ - \ you'll be working in more flour in a moment. Add too much flour now, and the extra\ - \ flour needed to roll out the noodles will lead to a dry rather than tender noodle.\n\ - \nMixed egg and flour kneaded together to form a shaggy dough\nTurn the dough out\ - \ onto a well-floured work surface. With well-floured hands, knead the dough, incorporating\ - \ more flour as necessary to keep it from sticking to either the work surface or\ - \ your hands, until the dough is smooth and firm and no longer sticky. This takes\ - \ roughly 5 to 10 minutes.\n\nFormed dough ball for egg pasta\nWrap the dough with\ - \ plastic wrap and chill it for at least 30 minutes and up to overnight.\n\nBall\ - \ of egg pasta dough in glass bowl covered with plastic wrap\nDivide the chilled\ - \ dough into 2 pieces and work with one half of the dough at a time.\n\nBall of\ - \ egg pasta dough cut in half with a knife\nOn a well-floured surface, roll out\ - \ the dough to the desired thickness (anywhere from 1/4 inch to paper-thin, depending\ - \ on your preference). Be sure to rotate or otherwise move the dough between each\ - \ pass of the rolling pin to keep the dough from sticking to the work surface underneath.\ - \ Sprinkle everything with flour\u2014including the work surface when you lift the\ - \ dough\u2014as necessary to keep the dough from sticking.\n\nEgg pasta dough rolled\ - \ out with wooden rolling pin\nUse a sharp knife or pizza cutting wheel to cut the\ - \ noodles. You can make them as narrow or wide as you like. Be sure to cut them\ - \ as evenly as possible to ensure a uniform cooking time. If you fold the dough\ - \ to cut, make sure it is floured so it does not stick together.\n\nFresh pasta\ - \ cut into noodles with a knife\nLay the noodles on a cooling or drying rack and\ - \ let them sit until ready to cook. Repeat rolling and cutting with the remaining\ - \ half of the dough.\n\nFresh homemade egg pasta noodles on a marble counter \n\ - Boil the noodles in well-salted water until tender to the bite (2 to 10 minutes\ - \ for fresh noodles depending on the thickness). Drain and use in your favorite\ - \ recipe. Enjoy!\n\nEgg pasta noodles with pesto and Parmesan cheese on a plate\n\ - \n" -raw_completion_output: "\nLabel: Homemade Egg Noodles \nDescription: Homemade egg\ - \ noodles that are boiled until tender for use in your favorite recipe.\nCategories:\ - \ Pasta; Noodles \nIngredients: Flour; Salt; Eggs \nSteps: Gather the ingredients;\ - \ Combine the flour and salt in a bowl/on a work surface and make a well in the\ - \ center; Beat eggs with a fork and gradually incorporate flour; Knead dough with\ - \ well-floured hands until smooth and firm; Wrap dough in plastic wrap and chill;\ - \ Divide chilled dough into two and roll out; Cut noodles; Boil in salted water\ - \ and drain; Enjoy." -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - none - - - === - - - ' -extracted_object: - label: Homemade Egg Noodles - description: Homemade egg noodles that are boiled until tender for use in your favorite - recipe. - categories: - - FOODON:03306347 - - FOODON:03306944 - ingredients: - - food_item: - food: FOODON:03301116 - - food_item: - food: AUTO:Salt - state: Chopped - - food_item: - food: FOODON:03316061 - steps: - - action: AUTO:Gather%3B - inputs: - - food: FOODON:00004272 - state: N/A - utensils: - - AUTO:N/A. - - action: AUTO:Combine - inputs: - - food: FOODON:03301116 - - food: AUTO:Salt - state: Chopped - outputs: - - food: AUTO:Well - utensils: - - AUTO:Bowl - - AUTO:Work%20surface - - action: AUTO:Beat%3B%20incorporate - inputs: - - food: FOODON:03316061 - - food: FOODON:03301116 - outputs: - - food: FOODON:03316061 - state: beaten - - food: FOODON:03301116 - state: incorporated - utensils: - - AUTO:fork - - action: AUTO:knead%3B - inputs: - - food: FOODON:03311552 - outputs: - - food: FOODON:03311552 - state: smooth and firm - utensils: - - AUTO:hands. - - action: AUTO:Wrap%3B%20Chill - inputs: - - food: FOODON:03311552 - outputs: - - food: FOODON:03311552 - utensils: - - AUTO:None - - action: AUTO:divide%3B%20roll%20out - inputs: - - food: FOODON:03311552 - state: chilled - outputs: - - food: AUTO:two%20pieces%20of%20dough - utensils: - - AUTO:none - - action: FOODON:00002777 - inputs: - - food: FOODON:03306944 - outputs: - - food: FOODON:03306944 - state: cut - utensils: - - AUTO:none - - action: AUTO:Boil%3B%20Drain - inputs: - - food: FOODON:00002340 - - food: AUTO:Salt - state: Chopped - outputs: - - food: AUTO:Boiled%20Water - state: Boiled - utensils: - - AUTO:Pot - - action: AUTO:none - inputs: - - food: AUTO:none - outputs: - - food: AUTO:none - utensils: - - AUTO:none -named_entities: -- id: AUTO:Main - label: Main -- id: FOODON:03306347 - label: Pasta -- id: FOODON:03301704 - label: onion -- id: AUTO:small%20%28chopped%29 - label: small (chopped) -- id: FOODON:00003485 - label: bell pepper -- id: AUTO:cups - label: cups -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: AUTO:salt - label: salt -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: FOODON:03000227 - label: tomato -- id: AUTO:%2815%20ounce%29%20cans - label: (15 ounce) cans -- id: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - label: 1 (16 ounce) box spaghetti noodles -- id: FOODON:00001282 - label: hamburger meat -- id: AUTO:lbs - label: lbs -- id: AUTO:Melt%3B%20Saut%C3%A9 - label: "Melt; Saut\xE9" -- id: AUTO:Pan - label: Pan -- id: AUTO:add%3B%20cook - label: add; cook -- id: AUTO:well%20done - label: well done -- id: AUTO:pan - label: pan -- id: AUTO:Add - label: Add -- id: AUTO:adjust%3B - label: adjust; -- id: FOODON:03460173 - label: salted -- id: AUTO:none - label: none -- id: AUTO:Cook - label: Cook -- id: FOODON:03306944 - label: noodles -- id: AUTO:Mix%3B - label: Mix; -- id: FOODON:03311146 - label: sauce -- id: HANCESTRO:0415 - label: Mexican -- id: AUTO:Soup - label: Soup -- id: AUTO:poached%20chicken - label: poached chicken -- id: AUTO:1%20%2815%20oz%29%20can%20fire%20roasted%20tomatoes - label: 1 (15 oz) can fire roasted tomatoes -- id: AUTO:N/A - label: N/A -- id: AUTO:red%20enchilada%20sauce - label: red enchilada sauce -- id: AUTO:oz - label: oz -- id: FOODON:03310943 - label: zucchini -- id: AUTO:medium%2C%20sliced%20into%201/4-inch%20half%20circles - label: medium, sliced into 1/4-inch half circles -- id: AUTO:1%20%284%20oz%29%20can%20green%20chilies - label: 1 (4 oz) can green chilies -- id: FOODON:03411457 - label: chicken -- id: AUTO:creamed%20corn - label: creamed corn -- id: AUTO:ground%20cumin - label: ground cumin -- id: AUTO:tsp - label: tsp -- id: FOODON:03302030 - label: chili powder -- id: AUTO:sea%20salt - label: sea salt -- id: AUTO:freshly%20ground%20black%20pepper - label: freshly ground black pepper -- id: AUTO:bay%20leaves - label: bay leaves -- id: AUTO:cilantro - label: cilantro -- id: AUTO:Tbsp - label: Tbsp -- id: FOODON:00003661 - label: lime -- id: FOODON:03302515 - label: sour cream -- id: FOODON:00001013 - label: cheese -- id: FOODON:00003600 - label: avocado -- id: AUTO:large%2C%20sliced - label: large, sliced -- id: FOODON:03310710 - label: Tortilla chips -- id: AUTO:Pick%3B - label: Pick; -- id: AUTO:pre-cooked%20chicken - label: pre-cooked chicken -- id: AUTO:meat - label: meat -- id: dbpediaont:Square - label: Place -- id: AUTO:large%20stock%20pot - label: large stock pot -- id: AUTO:Pot - label: Pot -- id: AUTO:add%3B - label: add; -- id: FOODON:03304007 - label: enchilada sauce -- id: FOODON:03317304 - label: chilis -- id: AUTO:corn - label: corn -- id: FOODON:00003024 - label: cumin -- id: AUTO:pot - label: pot -- id: AUTO:Stir%3B - label: Stir; -- id: AUTO:combine - label: combine -- id: AUTO:- - label: '-' -- id: AUTO:cook%3B - label: cook; -- id: AUTO:soup - label: soup -- id: AUTO:none. - label: none. -- id: AUTO:topping%3B - label: topping; -- id: AUTO:fresh%20lime%20juice - label: fresh lime juice -- id: FOODON:03302052 - label: corn chips -- id: FOODON:03301116 - label: Flour -- id: AUTO:Salt - label: Salt -- id: FOODON:03316061 - label: Eggs -- id: AUTO:Gather%3B - label: Gather; -- id: FOODON:00004272 - label: ingredients -- id: AUTO:N/A. - label: N/A. -- id: AUTO:Combine - label: Combine -- id: AUTO:Well - label: Well -- id: AUTO:Bowl - label: Bowl -- id: AUTO:Work%20surface - label: Work surface -- id: AUTO:Beat%3B%20incorporate - label: Beat; incorporate -- id: AUTO:fork - label: fork -- id: AUTO:knead%3B - label: knead; -- id: FOODON:03311552 - label: dough -- id: AUTO:hands. - label: hands. -- id: AUTO:Wrap%3B%20Chill - label: Wrap; Chill -- id: AUTO:None - label: None -- id: AUTO:divide%3B%20roll%20out - label: divide; roll out -- id: AUTO:two%20pieces%20of%20dough - label: two pieces of dough -- id: FOODON:00002777 - label: Cut -- id: AUTO:Boil%3B%20Drain - label: Boil; Drain -- id: FOODON:00002340 - label: Water -- id: AUTO:Boiled%20Water - label: Boiled Water diff --git a/tests/output/recipe-palak-paneer.owl b/tests/output/recipe-palak-paneer.owl deleted file mode 100644 index 71630dadd..000000000 --- a/tests/output/recipe-palak-paneer.owl +++ /dev/null @@ -1,337 +0,0 @@ -Prefix( owl: = ) -Prefix( rdf: = ) -Prefix( rdfs: = ) -Prefix( xsd: = ) -Prefix( xml: = ) -Prefix( linkml: = ) -Prefix( recipe: = ) -Prefix( FOODON: = ) -Prefix( UO: = ) -Prefix( dcterms: = ) -Prefix( HANCESTRO: = ) -Prefix( BFO: = ) -Prefix( AUTO: = ) -Prefix( RO: = ) -Prefix( qudt: = ) -Prefix( dbpediaont: = ) -Prefix( core: = ) -Prefix( shex: = ) - -Ontology( - EquivalentClasses( - AUTO:_ROOT - ObjectIntersectionOf( - recipe:Recipe - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) - ) - ) - Declaration( Class( AUTO:_ROOT ) ) - AnnotationAssertion( rdfs:label AUTO:_ROOT "Simple Spaghetti" ) - AnnotationAssertion( dcterms:description AUTO:_ROOT "An easy to make and delicious spaghetti dish." ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Main%20dishes ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Italian%20recipes ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - AnnotationAssertion( rdfs:label "bell pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "tomato sauce" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "onion" ) - AnnotationAssertion( rdfs:label "bell peppers" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "tomato" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "sauce" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "noodles" ) -) \ No newline at end of file diff --git a/tests/output/recipe-spaghetti.owl b/tests/output/recipe-spaghetti.owl deleted file mode 100644 index 71630dadd..000000000 --- a/tests/output/recipe-spaghetti.owl +++ /dev/null @@ -1,337 +0,0 @@ -Prefix( owl: = ) -Prefix( rdf: = ) -Prefix( rdfs: = ) -Prefix( xsd: = ) -Prefix( xml: = ) -Prefix( linkml: = ) -Prefix( recipe: = ) -Prefix( FOODON: = ) -Prefix( UO: = ) -Prefix( dcterms: = ) -Prefix( HANCESTRO: = ) -Prefix( BFO: = ) -Prefix( AUTO: = ) -Prefix( RO: = ) -Prefix( qudt: = ) -Prefix( dbpediaont: = ) -Prefix( core: = ) -Prefix( shex: = ) - -Ontology( - EquivalentClasses( - AUTO:_ROOT - ObjectIntersectionOf( - recipe:Recipe - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) - ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) - ) - ) - Declaration( Class( AUTO:_ROOT ) ) - AnnotationAssertion( rdfs:label AUTO:_ROOT "Simple Spaghetti" ) - AnnotationAssertion( dcterms:description AUTO:_ROOT "An easy to make and delicious spaghetti dish." ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Main%20dishes ) - AnnotationAssertion( dcterms:subject AUTO:_ROOT AUTO:Italian%20recipes ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:small%20onion ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "2" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "3" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1" ) - ObjectSomeValuesFrom( qudt:unit ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "canned" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "2" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles ) - DataHasValue( recipe:state "uncooked" ) - ) ) - ObjectSomeValuesFrom( recipe:amount DataHasValue( recipe:value "1" ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( recipe:food_item ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( recipe:amount ObjectIntersectionOf( - DataHasValue( recipe:value "1 - 1 1⁄2" ) - ObjectSomeValuesFrom( qudt:unit AUTO:lb ) - ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:melt%3B%20saut%C3%A9 - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B%20cook - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "chopped/diced" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:meat ) - DataHasValue( recipe:state "well done" ) - ) ) - ObjectSomeValuesFrom( AUTO:pan ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:add%3B - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "sauce" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:none ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:adjust - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:salt ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "powder" ) - ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( AUTO:inputs ) - DataHasValue( recipe:state "adjusted" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:Cook - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( AUTO:as%20directed ) ) - ) ) ) - SubClassOf( AUTO:_ROOT ObjectSomeValuesFrom( recipe:steps ObjectIntersectionOf( - AUTO:mix%3B - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectSomeValuesFrom( ) ) - ObjectSomeValuesFrom( ObjectIntersectionOf( - ObjectSomeValuesFrom( ) - DataHasValue( recipe:state "+" ) - ) ) - ObjectSomeValuesFrom( AUTO:none ) - ) ) ) - AnnotationAssertion( rdfs:label "bell pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "tablespoons" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "teaspoon" ) - AnnotationAssertion( rdfs:label "tomato sauce" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "butter" ) - AnnotationAssertion( rdfs:label "onion" ) - AnnotationAssertion( rdfs:label "bell peppers" ) - AnnotationAssertion( rdfs:label "hamburger meat" ) - AnnotationAssertion( rdfs:label "tomato" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "pepper" ) - AnnotationAssertion( rdfs:label "garlic" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "sauce" ) - AnnotationAssertion( rdfs:label "noodles" ) - AnnotationAssertion( rdfs:label "noodles" ) -) \ No newline at end of file diff --git a/tests/output/recipe-spaghetti.pickle b/tests/output/recipe-spaghetti.pickle deleted file mode 100644 index df48e1075..000000000 Binary files a/tests/output/recipe-spaghetti.pickle and /dev/null differ diff --git a/tests/output/recipe-spaghetti.yaml b/tests/output/recipe-spaghetti.yaml deleted file mode 100644 index d01824103..000000000 --- a/tests/output/recipe-spaghetti.yaml +++ /dev/null @@ -1,207 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt -input_text: "SIMPLE SPAGHETTI\n\nDIRECTIONS\nOn medium heat melt the butter and sautee\ - \ the onion and bell peppers.\nAdd the hamburger meat and cook until meat is well\ - \ done.\nAdd the tomato sauce, salt, pepper and garlic powder.\nSalt, pepper and\ - \ garlic powder can be adjusted to your own tastes.\nCook noodles as directed.\n\ - Mix the sauce and noodles if you like, I keep them separated.\n\nINGREDIENTS\nUNITS:\ - \ US\n1\nsmall onion (chopped)\n1\nbell pepper (chopped)\n2\ntablespoons garlic\ - \ powder\n3\ntablespoons butter\n1\nteaspoon salt\n1\nteaspoon pepper\n2\n(15 ounce)\ - \ cans tomato sauce\n1\n(16 ounce) box spaghetti noodles\n1 - 1 1\u20442\nlb hamburger\ - \ meat.\n" -raw_completion_output: "\nurl: \nlabel: Simple Spaghetti\ndescription: A recipe for\ - \ a simple spaghetti featuring saut\xE9ed onions, bell peppers and hamburger meat.\n\ - categories: Main; Pasta\ningredients: 1 small onion (chopped); 1 bell pepper (chopped);\ - \ 2 tablespoons garlic powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon\ - \ pepper; 2 (15 ounce) cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1\ - \ - 1 1\u20442 lb hamburger meat\nsteps: On medium heat melt the butter and saut\xE9\ - \ the onion and bell peppers; Add the hamburger meat and cook until well done; Add\ - \ the tomato sauce, salt, pepper and garlic powder; Salt, pepper and garlic powder\ - \ can be adjusted to own tastes; Cook noodles as directed; Mix the sauce and noodles\ - \ if desired." -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - noodles - - - === - - - ' -extracted_object: - label: Simple Spaghetti - description: "A recipe for a simple spaghetti featuring saut\xE9ed onions, bell\ - \ peppers and hamburger meat." - categories: - - AUTO:Main - - FOODON:03306347 - ingredients: - - food_item: - food: FOODON:03301704 - amount: - value: '1' - unit: AUTO:small%20%28chopped%29 - - food_item: - food: FOODON:00003485 - state: chopped - amount: - value: '4' - unit: AUTO:cups - - food_item: - food: FOODON:00003582 - state: powder - amount: - value: '2' - unit: UO:0010042 - - food_item: - food: FOODON:03310351 - amount: - value: '3' - unit: UO:0010042 - - food_item: - food: AUTO:salt - amount: - value: '1' - unit: UO:0010040 - - food_item: - food: FOODON:00001649 - amount: - value: '1' - unit: UO:0010040 - - food_item: - food: FOODON:03000227 - state: sauce - amount: - value: '2' - unit: AUTO:%2815%20ounce%29%20cans - - food_item: - food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - state: uncooked - amount: - value: '1' - - food_item: - food: FOODON:00001282 - state: chopped - amount: - value: "1 - 1 1\u20442" - unit: AUTO:lbs - steps: - - action: AUTO:Melt%3B%20Saut%C3%A9 - inputs: - - food: FOODON:03310351 - - food: FOODON:03301704 - - food: FOODON:00003485 - state: diced - utensils: - - AUTO:Pan - - action: AUTO:add%3B%20cook - inputs: - - food: FOODON:00001282 - state: chopped - outputs: - - food: AUTO:well%20done - state: done - utensils: - - AUTO:pan - - action: AUTO:Add - inputs: - - food: FOODON:03000227 - state: sauce - - food: AUTO:salt - - food: FOODON:00001649 - - food: FOODON:00003582 - state: powder - - action: AUTO:adjust%3B - inputs: - - food: AUTO:salt - - food: FOODON:00001649 - - food: FOODON:00003582 - state: powder - outputs: - - food: FOODON:03460173 - - food: FOODON:00001649 - state: peppered - - food: FOODON:00003582 - state: flavoured - utensils: - - AUTO:none - - action: AUTO:Cook - inputs: - - food: FOODON:03306944 - outputs: - - food: AUTO:none - utensils: - - AUTO:none - - action: AUTO:Mix%3B - inputs: - - food: FOODON:03311146 - - food: FOODON:03306944 -named_entities: -- id: AUTO:Main - label: Main -- id: FOODON:03306347 - label: Pasta -- id: FOODON:03301704 - label: onion -- id: AUTO:small%20%28chopped%29 - label: small (chopped) -- id: FOODON:00003485 - label: bell pepper -- id: AUTO:cups - label: cups -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: AUTO:salt - label: salt -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: FOODON:03000227 - label: tomato -- id: AUTO:%2815%20ounce%29%20cans - label: (15 ounce) cans -- id: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - label: 1 (16 ounce) box spaghetti noodles -- id: FOODON:00001282 - label: hamburger meat -- id: AUTO:lbs - label: lbs -- id: AUTO:Melt%3B%20Saut%C3%A9 - label: "Melt; Saut\xE9" -- id: AUTO:Pan - label: Pan -- id: AUTO:add%3B%20cook - label: add; cook -- id: AUTO:well%20done - label: well done -- id: AUTO:pan - label: pan -- id: AUTO:Add - label: Add -- id: AUTO:adjust%3B - label: adjust; -- id: FOODON:03460173 - label: salted -- id: AUTO:none - label: none -- id: AUTO:Cook - label: Cook -- id: FOODON:03306944 - label: noodles -- id: AUTO:Mix%3B - label: Mix; -- id: FOODON:03311146 - label: sauce diff --git a/tests/output/recipe-tortilla-soup.pickle b/tests/output/recipe-tortilla-soup.pickle deleted file mode 100644 index 58e540545..000000000 Binary files a/tests/output/recipe-tortilla-soup.pickle and /dev/null differ diff --git a/tests/output/recipe-tortilla-soup.yaml b/tests/output/recipe-tortilla-soup.yaml deleted file mode 100644 index fc574b578..000000000 --- a/tests/output/recipe-tortilla-soup.yaml +++ /dev/null @@ -1,444 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-tortilla-soup.txt -input_text: 'Tortilla Soup - - - Ingredients - - 1 rotisserie chicken or 3-4 cups poached chicken - - 1 (15 oz) can fire roasted tomatoes, diced - - 1 (10 oz) can red enchilada sauce, mild - - 1 small onion, chopped - - 1 medium zucchini, sliced into 1/4-inch half circles - - 1 (4 oz) can green chilies - - 4 cloves garlic, minced - - 4 cups chicken broth - - 1 (14.5 oz) can creamed corn, undrained (can sub with 1 can sweet corn, drained) - - 1 tsp ground cumin - - 1 tsp chili powder - - 1 tsp sea salt - - 1/4 tsp freshly ground black pepper - - 3 bay leaves - - - Garnish - - 4 Tbsp chopped cilantro - - 1 lime cut into wedges - - sour cream - - cheese, shredded (cheddar, mozzarella, Mexican blend) - - 1 large avocado, sliced - - Tortilla chips, crushed - - - Method - - While rotisserie chicken is still warm, pick all meat of the bones, discard skin. - Place the chicken meat in a large stock pot. Discard bones, or save if you like - to make homemade stock. - - Add to the pot the tomatoes, enchilada sauce, chicken broth, onion, zucchini, chilis, - garlic, corn, cumin, chili powder, salt, pepper and bay leaves. Stir to combine - and turn the heat to high. - - As soon as soup begins to boil, turn the heat to medium-low heat and continue to - cook, uncovered, until the onions are translucent and zucchini is tender, about - 30 minutes. - - Serve the soup topped with chopped cilantro, a squeeze of fresh lime juice, sour - cream, cheese, avocado and corn chips. - - ' -raw_completion_output: "\nurl: \nlabel: Tortilla Soup\ndescription: This is a traditional\ - \ Mexican soup that can be made with a rotisserie chicken or poached chicken. It\ - \ is full of flavor and garnished with cilantro, lime juice, sour cream, cheese,\ - \ avocado, and corn chips. \ncategories: Mexican; Soup\ningredients: 1 rotisserie\ - \ chicken or 3-4 cups poached chicken; 1 (15 oz) can fire roasted tomatoes, diced;\ - \ 1 (10 oz) can red enchilada sauce, mild; 1 small onion, chopped; 1 medium zucchini,\ - \ sliced into 1/4-inch half circles; 1 (4 oz) can green chilies; 4 cloves garlic,\ - \ minced; 4 cups chicken broth; 1 (14.5 oz) can creamed corn, undrained (can sub\ - \ with 1 can sweet corn, drained); 1 tsp ground cumin; 1 tsp chili powder; 1 tsp\ - \ sea salt; 1/4 tsp freshly ground black pepper; 3 bay leaves; 4 Tbsp chopped cilantro;\ - \ 1 lime cut into wedges; sour cream; cheese, shredded (cheddar, mozzarella, Mexican\ - \ blend); 1 large avocado, sliced; Tortilla chips, crushed\nsteps: Pick all meat\ - \ of the bones from pre-cooked chicken, discard skin and bones; Place chicken meat\ - \ into large stock pot; Add tomatoes, enchilada sauce, chicken broth, onion, zucchini,\ - \ chilis, garlic, corn, cumin, chili powder, salt, pepper and bay leaves to pot;\ - \ Stir to combine and turn the heat to high; As soon as soup begins to boil, turn\ - \ the heat to medium-low and cook uncovered until onions are translucent and zucchini\ - \ is tender, about 30 minutes; Serve soup topped with chopped cilantro, a squeeze\ - \ of fresh lime juice, sour cream, cheese, avocado and corn chips." -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - soup - - - === - - - ' -extracted_object: - label: Tortilla Soup - description: This is a traditional Mexican soup that can be made with a rotisserie - chicken or poached chicken. It is full of flavor and garnished with cilantro, - lime juice, sour cream, cheese, avocado, and corn chips. - categories: - - HANCESTRO:0415 - - AUTO:Soup - ingredients: - - food_item: - food: AUTO:poached%20chicken - state: poached - amount: - value: 3-4 - unit: AUTO:cups - - food_item: - food: AUTO:1%20%2815%20oz%29%20can%20fire%20roasted%20tomatoes - state: chopped - amount: - value: diced - unit: AUTO:N/A - - food_item: - food: AUTO:red%20enchilada%20sauce - state: chopped - amount: - value: '10' - unit: AUTO:oz - - food_item: - food: FOODON:03301704 - state: small - amount: - value: chopped - unit: AUTO:N/A - - food_item: - food: FOODON:03310943 - state: chopped - amount: - value: '1' - unit: AUTO:medium%2C%20sliced%20into%201/4-inch%20half%20circles - - food_item: - food: AUTO:1%20%284%20oz%29%20can%20green%20chilies - state: chopped, diced - amount: - value: '1' - - food_item: - food: FOODON:00003582 - state: cloves - amount: - value: minced - - food_item: - food: FOODON:03411457 - state: broth - amount: - value: '4' - unit: AUTO:cups - - food_item: - food: AUTO:creamed%20corn - state: creamed - amount: - value: '14.5' - unit: AUTO:oz - - food_item: - food: AUTO:ground%20cumin - state: ground - amount: - value: '1' - unit: AUTO:tsp - - food_item: - food: FOODON:03302030 - state: chopped - amount: - value: '1' - unit: AUTO:tsp - - food_item: - food: AUTO:sea%20salt - state: diced - amount: - value: '1' - unit: AUTO:tsp - - food_item: - food: AUTO:freshly%20ground%20black%20pepper - state: ground - amount: - value: 1/4 - unit: AUTO:tsp - - food_item: - food: AUTO:bay%20leaves - state: chopped - - food_item: - food: AUTO:cilantro - state: chopped - amount: - value: '4' - unit: AUTO:Tbsp - - food_item: - food: FOODON:00003661 - amount: - value: '1' - - food_item: - food: FOODON:03302515 - state: chopped - - food_item: - food: FOODON:00001013 - state: shredded (cheddar, mozzarella, Mexican blend) - - food_item: - food: FOODON:00003600 - amount: - value: '1' - unit: AUTO:large%2C%20sliced - - food_item: - food: FOODON:03310710 - state: Chopped - amount: - value: crushed - steps: - - action: AUTO:Pick%3B - inputs: - - food: AUTO:pre-cooked%20chicken - state: pre-cooked - outputs: - - food: AUTO:meat - utensils: - - AUTO:none - - action: dbpediaont:Square - inputs: - - food: FOODON:03411457 - state: meat - outputs: - - food: AUTO:large%20stock%20pot - utensils: - - AUTO:Pot - - action: AUTO:add%3B - inputs: - - food: FOODON:03000227 - - food: FOODON:03304007 - - food: FOODON:03411457 - state: broth - - food: FOODON:03301704 - - food: FOODON:03310943 - state: chopped - - food: FOODON:03317304 - state: chopped - - food: FOODON:00003582 - - food: AUTO:corn - - food: FOODON:00003024 - state: chopped - - food: FOODON:03302030 - state: chopped - - food: AUTO:salt - - food: FOODON:00001649 - - food: AUTO:bay%20leaves - outputs: - - food: AUTO:pot - utensils: - - AUTO:pot - - action: AUTO:Stir%3B - inputs: - - food: AUTO:combine - utensils: - - AUTO:- - - action: AUTO:cook%3B - inputs: - - food: AUTO:soup - outputs: - - food: FOODON:03310943 - state: diced - utensils: - - AUTO:none. - - action: AUTO:topping%3B - inputs: - - food: AUTO:cilantro - state: chopped - - food: AUTO:fresh%20lime%20juice - state: chopped - - food: FOODON:03302515 - state: chopped - - food: FOODON:00001013 - - food: FOODON:00003600 - - food: FOODON:03302052 - state: chopped - outputs: - - food: AUTO:soup - utensils: - - AUTO:none -named_entities: -- id: AUTO:Main - label: Main -- id: FOODON:03306347 - label: Pasta -- id: FOODON:03301704 - label: onion -- id: AUTO:small%20%28chopped%29 - label: small (chopped) -- id: FOODON:00003485 - label: bell pepper -- id: AUTO:cups - label: cups -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: AUTO:salt - label: salt -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: FOODON:03000227 - label: tomato -- id: AUTO:%2815%20ounce%29%20cans - label: (15 ounce) cans -- id: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - label: 1 (16 ounce) box spaghetti noodles -- id: FOODON:00001282 - label: hamburger meat -- id: AUTO:lbs - label: lbs -- id: AUTO:Melt%3B%20Saut%C3%A9 - label: "Melt; Saut\xE9" -- id: AUTO:Pan - label: Pan -- id: AUTO:add%3B%20cook - label: add; cook -- id: AUTO:well%20done - label: well done -- id: AUTO:pan - label: pan -- id: AUTO:Add - label: Add -- id: AUTO:adjust%3B - label: adjust; -- id: FOODON:03460173 - label: salted -- id: AUTO:none - label: none -- id: AUTO:Cook - label: Cook -- id: FOODON:03306944 - label: noodles -- id: AUTO:Mix%3B - label: Mix; -- id: FOODON:03311146 - label: sauce -- id: HANCESTRO:0415 - label: Mexican -- id: AUTO:Soup - label: Soup -- id: AUTO:poached%20chicken - label: poached chicken -- id: AUTO:1%20%2815%20oz%29%20can%20fire%20roasted%20tomatoes - label: 1 (15 oz) can fire roasted tomatoes -- id: AUTO:N/A - label: N/A -- id: AUTO:red%20enchilada%20sauce - label: red enchilada sauce -- id: AUTO:oz - label: oz -- id: FOODON:03310943 - label: zucchini -- id: AUTO:medium%2C%20sliced%20into%201/4-inch%20half%20circles - label: medium, sliced into 1/4-inch half circles -- id: AUTO:1%20%284%20oz%29%20can%20green%20chilies - label: 1 (4 oz) can green chilies -- id: FOODON:03411457 - label: chicken -- id: AUTO:creamed%20corn - label: creamed corn -- id: AUTO:ground%20cumin - label: ground cumin -- id: AUTO:tsp - label: tsp -- id: FOODON:03302030 - label: chili powder -- id: AUTO:sea%20salt - label: sea salt -- id: AUTO:freshly%20ground%20black%20pepper - label: freshly ground black pepper -- id: AUTO:bay%20leaves - label: bay leaves -- id: AUTO:cilantro - label: cilantro -- id: AUTO:Tbsp - label: Tbsp -- id: FOODON:00003661 - label: lime -- id: FOODON:03302515 - label: sour cream -- id: FOODON:00001013 - label: cheese -- id: FOODON:00003600 - label: avocado -- id: AUTO:large%2C%20sliced - label: large, sliced -- id: FOODON:03310710 - label: Tortilla chips -- id: AUTO:Pick%3B - label: Pick; -- id: AUTO:pre-cooked%20chicken - label: pre-cooked chicken -- id: AUTO:meat - label: meat -- id: dbpediaont:Square - label: Place -- id: AUTO:large%20stock%20pot - label: large stock pot -- id: AUTO:Pot - label: Pot -- id: AUTO:add%3B - label: add; -- id: FOODON:03304007 - label: enchilada sauce -- id: FOODON:03317304 - label: chilis -- id: AUTO:corn - label: corn -- id: FOODON:00003024 - label: cumin -- id: AUTO:pot - label: pot -- id: AUTO:Stir%3B - label: Stir; -- id: AUTO:combine - label: combine -- id: AUTO:- - label: '-' -- id: AUTO:cook%3B - label: cook; -- id: AUTO:soup - label: soup -- id: AUTO:none. - label: none. -- id: AUTO:topping%3B - label: topping; -- id: AUTO:fresh%20lime%20juice - label: fresh lime juice -- id: FOODON:03302052 - label: corn chips diff --git a/tests/output/spires-extract-spaghetti.owl b/tests/output/spires-extract-spaghetti.owl deleted file mode 100644 index 59ac5c179..000000000 --- a/tests/output/spires-extract-spaghetti.owl +++ /dev/null @@ -1,7689 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - label - label - label - label - - - - - - - - - - - - - - - - - - - - - - - - - is part of - a core relation that holds between a part and its whole - - part of - part of - part_of - - - - - - - - - - has part - a core relation that holds between a whole and its part - - - has part - has part - has_part - - - - - - - - - A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. - Damion Dooley - FoodOn - For example, 'bean soup' has a defining ingredient of some 'bean (whole)'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. - -A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. - has defining ingredient - - - - - - - - - - - A relation attaching between a food material and another food material that has been added to it at some point in its history. - Damion Dooley - FoodOn - has ingredient - - - - - - - - - participates in - a relation between a continuant and a process, in which the continuant is somehow involved in the process - - - participates in - participates_in - - - - - - - - has participant - a relation between a process and a continuant, in which the continuant is somehow involved in the process - - has participant - has_participant - - - - - - - - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - - has quality - - - - - - - - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - - has role - - - - - - - - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - - derives from - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - in taxon - - - - - - - - - develops from - develops from - develops_from - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - has input - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - has output - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - - member of - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - - produced by - - - - - - - - - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - Damion Dooley - - has substance added - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - canned - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - 1-1 1⁄2 - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - well done - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to own tastes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - - - - - - - - - - - - canned - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1-1 1⁄2 - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - chopped, diced - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped/diced - - - - - - - - - - - - - - - - - well done - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - powder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - to own tastes - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - chopped - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A classic spaghetti recipe made with onion, bell peppers, garlic powder, butter, salt, pepper, tomato sauce, and hamburger meat. - - - Simple Spaghetti - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - material - MaterialEntity - material entity - material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - bfo - BFO:0000040 - - material entity - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - A role played by the molecular entity or part thereof within a biological context. - - biological role - - - - - - - - - food role - A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life. - - food - - - - - - - - role (CHEBI) - A role is particular behaviour which a material entity may exhibit. - - role - - - - - - - - - - physiological role - - - - - - - - - A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. - - environmental - environmental material - - - - - - - - - Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. - Damion Dooley - Foodon product type - https://en.wikipedia.org/wiki/Food - The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations. - food product - - - - - - - - - - - - - - - - - - - - - - A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. - - SUBSET_SIREN:F17332 - mammalian meat food product - - - - - - - - - - - - - - - - - - - - - - - - - - - This class includes food products which are derived from or produced by a plant. - plant food product - - - - - - - - - - - - - - - - - - - - - - - - - - Meat from bovines, especially domestic cattle (cows). - beef food product - - - - - Meat from bovines, especially domestic cattle (cows). - http://en.wikipedia.org/wiki/Beef - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product derived from plant fruit. - plant fruit food product - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product which is derived from or produced by an animal that has a vertibrae. - Damion Dooley - vertebrate animal food product - - - - - - - - - bovine dairy food product - - - - - - - - - - - - - - - cattle dairy food product - - - - - - - - - - - - - - - A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. - Damion Dooley - https://en.wikipedia.org/wiki/Condiment - condiment - condiment food product - - - - - - - - - - - - - - - - - - - - - - - - - - bovine meat food product - - - - - - - - - A food product derived from or produced by a plant root. - plant root food product - - - - - - - - - - solanaceous fruit food product - - - - - - - - - - - - - - - - A food product deriving from one or more tomatoes. - tomato food product - - - - - - - - - solanaceous food product - - - - - - - - - - - - - - - - - - - - - - - - - - invertebrate animal food product - - - - - - - - - - - - - - - - - A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. - Damion Dooley - http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 - http://www.langual.org/langual_thesaurus.asp?termid=H0151 - herb and spice - herb or spice - spice or herb - - - - - - - - - - - - - - - - - - - - - - A dairy food product has mammilian milk or a milk component as an ingredient. - Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=H0242 - dairy product - milk product - dairy food product - - - - - - - - - milk or milk based food product - - - - - - - - - - - - - - - - - - - - - - Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. - - vegetable food product - - - - - - - - - - A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. - - - beef mince - beef mince - ground beef - hamburger meat - minced beef - ground beef food product - - - - - - - - - pepper - black or white pepper product - - - - - - - - - A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. - food product component - - - - - - - - - - - - - - - - - - - - - - - - - - - cow milk based food product - - - - - - - - - cow milk butter food product - - - - - - - - - - - - - - - - - - - - - - - - - - - garlic food product - - - - - - - - - - - - - - - - - - - - - - - - - - ginger - ginger food product - - - - - - - - - - - - - - - gravy or sauce - - - - - - - - - - - - - - - - - - - - - - - - - - green bell pepper food product - - - - - - - - - - - - - - - - - - - - - - - - - - red pepper - hot pepper food product - - - - - - - - - - - - - - - - - - - - - - - - - - milk based gravy or sauce food product - - - - - - - - - - - - - - - - - - - - - - - - - - - onion flavouring food product - - - - - - - - - - - - - - - - - - - - - - - - - - onion food product - - - - - - - - - - - - - - - A food product deriving from one or more sweet or hot peppers. - pepper vegetable food product - - - - - - - - - plant based gravy or sauce food product - - - - - - - - - - - - - - - A plant fruit food product which is labeled (in common language or by regulation) as a vegetable food product. - plant fruit as vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product harvested from underground plant parts. - plant root vegetable food product - - - - - - - - - - - - - - - - - - - - - - - - - - red bell pepper food product - - - - - - - - - - - - - - - tomato based gravy or sauce food product - - - - - - - - - - - - - - - tomato substance - - - - - - - - - vegetable based gravy or sauce food product - - - - - - - - - - - - - - - A food product consisting of food material derived primarily from a single organism. - Damion Dooley - food product by organism - - - - - - - - - - - - - - - - - - - - - - - - - - Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience - - - food - foodstuff - nourishment - sustenance - food material - - - - - - - - - Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] - - Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. - Damion Dooley - https://en.wikipedia.org/wiki/Invertebrate - animal - invertebrate animal - - - - - - - - - - A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. - Damion Dooley - food product by quality - - - - - - - - - - - - - - - - - - - - - - A food product consisting of food material derived from ingredients sourced from multiple organisms. - Damion Dooley - 2019-01-23T22:40:32Z - multi-ingredient - The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 - -Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? - multi-component food product - - - - - - - - - - Dairy cattle are a type of cattle bred for the ability to produce large quantities of milk, from which dairy products are made. This class covers both male and female members of a dairy breed. - Damion Dooley - https://en.wikipedia.org/wiki/Dairy_cattle - 2019-01-26T22:49:27Z - dairy cattle - https://en.wikipedia.org/wiki/List_of_dairy_cattle_breeds - - - - - - - - - - Taurine cattle (Bos taurus taurus), also called European cattle, are a subspecies of domesticated cattle originating in the Near East. Both taurine cattle and indicine cattle (zebus) are descended from the aurochs. Taurine cattle were originally considered a distinct species, but are now typically grouped with zebus and aurochs into one species, Bos taurus. Most modern breeds of cattle are taurine cattle. - Damion Dooley - https://en.wikipedia.org/wiki/Taurine_cattle - 2019-01-28T02:41:04Z - http://www.langual.org/langual_thesaurus.asp?termid=B5186 - taurine cattle - - - - - - - - - Damion Dooley - 2019-06-28T00:25:22Z - ginger - ginger root - - - - - - - - - - - - - - - - - - - - - - - - - - - The poblano (Capsicum annuum) is a mild chili pepper originating in the state of Puebla, Mexico. Dried, it is called ancho or chile ancho, from the Spanish word ancho ("wide"). - - Emma Griffiths - 2019-08-13T04:55:19Z - ancho - ancho pepper - chile ancho - poblano - ancho pepper - - - - - - - - - - A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. - - - 2019-08-14T18:02:36Z - - animal - - - - - - - - - - - - - - - - - - - - - - - - - - - A bell pepper is a fruits in different colours - including red, yellow, orange, green, white, and purple - from a bell pepper plant cultivar. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". - - - 2019-08-22T18:01:49Z - - pepper - bell pepper food product - - - - - - - Kham Tran - www.khamtran.com - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). - - https://en.wikipedia.org/wiki/Vegetarian_cuisine - 2019-09-11T21:12:43Z - vegetarian food - vegetarian food product - - - - - - - - - - A food product made from black, white, pink or similar peppercorns. - - 2019-11-15T23:03:24Z - peppercorn food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A ripened red colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T12:37:01 - bell pepper - capsicum - pepper - sweet pepper - sweet red bell pepper - sweet red bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a pepper plant (Capsicum) - - https://orcid.org/0000-0001-5275-8866 - https://www.britannica.com/plant/pepper-plant-Capsicum-genus - 2020-10-14T02:39:11 - pepper - peppers - pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit in the Grossum cultivar group of a bell pepper plant. - - 2020-11-19T01:08:58Z - bell pepper - capsicum - pepper - sweet pepper - bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immature green colored berry fruit of a bell pepper plant cultivar. - - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T07:08:14 - bell pepper - capsicum - pepper - sweet green pepper - sweet pepper - sweet green bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A mature yellow colored berry fruit of a bell pepper plant cultivar. - - 2020-11-19T01:24:18Z - bell pepper - capsicum - pepper - sweet pepper - sweet yellow pepper - sweet yellow bell pepper (whole) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of a garlic plant (Allium sativum) - - https://en.wikipedia.org/wiki/Garlic - 2020-11-30T04:49:32 - garlic - garlic bulb - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A root of a ginger plant (Zingiber officinale) - - https://en.wikipedia.org/wiki/Ginger - 2021-02-11T17:33:19 - elephant ginger - elephant ginger root - ginger - ginger root - ginger root (whole) - - - - - - - - - - An anatomical part of a plant that is consumed by humans or other animals as food. - - https://en.wikipedia.org/wiki/Vegetable - 2021-02-12T18:49:32 - vegetable (whole) - - - - - - - - - - A plan specification for making a food product, which may have ingredient, device, action and objective specifications. - - 2021-11-29T21:52:28Z - food recipe - - - - - - - - - A food product deriving from one or more animals. - - 2022-09-01T16:31:09Z - animal food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole ginger root or some substance made from a processed ginger root. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Ginger - ginger - ginger root - ginger root (whole or parts) - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole tomato or some substance made from a processed tomato. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Tomato - 2022-04-13T12:27:40Z - tomato - tomato (whole or parts) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1217 - subset_siren - SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - tomato sauce - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A berry fruit of a tomato plant (Solanum lycopersicum). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F1453 - tomato - subset_siren - tomato (whole) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F1704 - onion - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion (whole, raw) - - - - - - - - - - - - - - - - - - - - http://langual.org - 2019-08-26T14:29:56Z - SUBSET_SIREN:F1886 - SUBSET_SIREN:F5599 - raw beef hamburger - subset_siren - SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) - - ground beef (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - Fruit which has not been subjected to heat treatment, but which may have other mechanical processes such as slicing applied to it. - http://langual.org - SUBSET_SIREN:F2007 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F2008 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - vegetable (raw) - - - - - - - - - - - http://langual.org - milk - SUBSET_SIREN:F2116 - cow milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - cow milk (liquid) - - - - - - - - - - - - - - - - - - - Note that this allows for several kinds of fruit in one sample, e.g. "some fruit (whole,raw)" allows "apple (whole, raw)" and "orange (whole, raw)". - Damion Dooley - http://langual.org - SUBSET_SIREN:F4644 - fruit - fruits - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit (whole, raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F6429 - subset_siren - SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - - meat (raw) - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - raw milk - SUBSET_SIREN:F7455 - milk - subset_siren - SIREN DB annotation: -* has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* has consumer 'not pasteurized claim or use' (http://purl.obolibrary.org/obo/FOODON_03510121) - - cow milk (raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9840 - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - ginger root (whole, raw) - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F9927 - garden tomato - tomato - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) -* derives from 'fruit, peel present, core, pit or seed present' (http://purl.obolibrary.org/obo/FOODON_03420140) - - tomato (whole, raw) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F10351 - subset_siren - SIREN DB annotation: -* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119) -* has quality 'partially heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440018) -* derives from 'butter' (http://purl.obolibrary.org/obo/FOODON_00001023) -* formed as a result of 'pasteurization by heating' (http://purl.obolibrary.org/obo/FOODON_03470135) - - butter - - - - - - - - - - - A food product that has not been cooked. - http://langual.org - SUBSET_SIREN:F11126 - subset_siren - SIREN DB annotation: -* has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) - - food (raw) - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F11146 - subset_siren - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - sauce - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15150 - subset_siren - SIREN DB annotation: -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - - mammalian milk product - - - - - - - - - - - - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15295 - subset_siren - SIREN DB annotation: -* has quality 'semiliquid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430135) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* formed as a result of 'alcohol-acetic acid fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460123) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - catsup - - - - - - - - - - - - - - - - - - - - - - - - - - - - A whole vegetable or some substance made from a processed vegetable. - https://orcid.org/0000-0001-5275-8866 - https://en.wikipedia.org/wiki/Vegetable - 2022-04-13T09:20:12Z - vegetable - vegetable (whole or parts) - - - - - - - - - - http://langual.org - SUBSET_SIREN:F15615 - subset_siren - SIREN DB annotation: -* derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) - - fruit food product - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A bulb of an onion plant (Allium cepa). - https://orcid.org/0000-0001-5275-8866 - http://langual.org - 2020-10-21T05:43:41 - SUBSET_SIREN:F16347 - bulb onion - common onion - subset_siren - SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'root, tuber or bulb, with peel' (http://purl.obolibrary.org/obo/FOODON_03420239) - - onion (whole) - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16522 - subset_siren - SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - tomato multi-component product - - - - - - - - - - - - - - - - http://langual.org - SUBSET_SIREN:F16579 - subset_siren - SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - - multi-component plant food product - - - - - - - - - - A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). - http://langual.org - SUBSET_SIREN:F17170 - subset_siren - SIREN DB annotation: -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - meat (whole or parts) - - - - - - - - - - Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0105 - condiment, dressing, gravy or sauce - gravy, condiment, dressing or sauce - sauce, condiment, dressing or gravy - dressing, condiment, gravy or sauce (us cfr) - - - - - - - - - - Aromatic or pungent plant product used whole or ground as a seasoning in food products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0113 - herb or spice - spice or herb (us cfr) - - - - - - - - - - Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0133 - seasoning or flavoring - flavoring or seasoning (us cfr) - - - - - - - - - - A multiple-component food product typically containing a protein source, a vegetable, and a potato, rice or cereal-based component packaged to be served after heating, either as separate items or courses or mixed as recipe components; see 21 CFR 102.26, 102.28 and 104.47 for nutritional quality guidelines. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0139 - compartmentalized dinner - dinner with components separated in serving containers - dinner, compartmentalized - food packs with separate components - heat and serve dinner - multiple-course dinner - tv dinner - multicomponent meal (us cfr) - - - - - - - - - - Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0143 - pie filling, fruit - fruit or fruit product (us cfr) - - - - - - - - - - Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0148 - milk or milk product (us cfr) - - - - - - - - - - Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0150 - meat or meat product (from mammal) (us cfr) - - - - - - - - - - Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0152 - vegetable or vegetable product (us cfr) - - - - - - - - - - Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0164 - dairy product (us cfr) - - - - - - - - - - Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0172 - prepared dish - prepared food product (us cfr) - - - - - - - - - - Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0179 - relish or condiment - condiment or relish (us cfr) - - - - - - - - - - Products of the flesh of animals. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0217 - meat, poultry, seafood or related product (us cfr) - - - - - - - - - - Fruits and vegetables in all forms. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0257 - fruit or vegetable product (us cfr) - - - - - - - - - - Nonstandardized food product used as a meal accompaniment and consisting of a mixture of fats or oils, starch, liquid and other optional ingredients specified by the recipe; excludes condiment sauce (q.v.) and tomato or spaghetti sauce, which are vegetable products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0286 - sauce or gravy - gravy or sauce (us cfr) - - - - - - - - - - Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0289 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - USA agency food product type - - - - - - - - - - An agency food product type is a class of food product defined by an agency or consortium. - Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0361 - This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. - agency food product type - - - - - - - - - - Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1270 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - U.S. code of federal regulations, title 21 food product type - https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1006 - fruit plant used as vegetable - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1018 - vegetable-producing plant, root, tuber or bulb - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1057 - vegetable-producing plant, above-ground parts - - - - - - - - - - Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. - Damion Dooley - https://en.wikipedia.org/wiki/Mammal - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1134 - mammal - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1140 - fruit-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1179 - flavor-producing plant - herb-producing plant - spice or flavor-producing plant - - - - - - - - - - - - - - - - - - - - - A dairy cow is an adult female member of a dairy cattle breed - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1201 - cow - domesticated cattle - dairy cow - - - - - - - - - - - - The taxonomies given vary widely. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1250 - capsicum - capsicum annuum - green or red pepper plant - - - - - - - - - - - - - - - - - The word "tomato" may refer to the plant (*Solanum lycopersicum*) or the edible, typically red, fruit that it bears. Originating in South America, the tomato was spread around the world following the Spanish colonization of the Americas, and its many varieties are now widely grown, often in greenhouses in cooler climates.See also the list of tomato cultivars - WIKIPEDIA:List_of_tomato_cultivars - http://langual.org - - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - PLANTS:SOLY2 - http://eol.org/pages/392557 - http://www.langual.org/langual_thesaurus.asp?termid=B1276 - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - gold apple - love apple - lycopersicon esculentum - lycopersicon lycopersicum - solanum lycopersicum - tomato plant - - - - - - - - - - A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. - Damion Dooley - - http://langual.org - animal - http://www.langual.org/langual_thesaurus.asp?termid=B1297 - LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. - vertebrate animal - - - - - - - - - - - - The onion (*Allium cepa *L), also known as the bulb onion or common onion, is a vegetable that is the most widely cultivated species of the genus *Allium*. Its close relatives include the garlic, shallot, leek, chive,[2] and Chinese onion. - This genus also contains several other species variously referred to as onions and cultivated for food, such as the Japanese bunching onion (*Allium fistulosum*), the tree onion (*A. ×proliferum*), and the Canada onion (*Allium canadense*). The name "wild onion" is applied to a number of *Allium* species, but *A. cepa* is exclusively known from cultivation. [https://en.wikipedia.org/wiki/Onion] - http://langual.org - GRIN:300022 - PLANTS:ALLIU - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B1300 - Allium - Allium L. - Allium sp. - allium spp. - bulb onion - cebolla - garden onion - onion plant - - - - - - - - - - This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. - http://langual.org - - http://www.langual.org/langual_thesaurus.asp?termid=B1564 - This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. - food product organismal source - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1579 - vegetable-producing plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1643 - capsicum annuum, longum group - capsicum chile pepper - cayenne pepper - chile pepper - chili pepper - long pepper - red pepper (chile pepper) - hot pepper plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2559 - pepper, poblano - poblano pepper plant - - - - - - - - - - - - - - - - - - - - - - - - - The bell pepper (also known as sweet pepper or pepper in the United Kingdom, Canada and Ireland, and capsicum in Australia, India, Pakistan, Bangladesh, Singapore and New Zealand) is a cultivar group of the species *Capsicum annuum*. Bell peppers are sometimes grouped with less pungent pepper varieties as "sweet peppers". [https://en.wikipedia.org/wiki/Bell_pepper] - http://langual.org - - GRIN:311784 - GRIN:8904 - ITIS:30492 - MANSFELD:6120 - PLANTS:CAAN4 - http://eol.org/pages/581098 - http://www.langual.org/langual_thesaurus.asp?termid=B2628 - sweet pepper plant - Capsicum annuum L. - Capsicum anuum L. - capsicum frutescens var. grossum - bell pepper plant - - - - - - - - - - Unripe fruit of red or yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2629 - green pepper plant - green bell pepper plant - - - - - - - - - - Ripe fruit of red bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2630 - red bell sweet pepper plant - red sweet pepper plant - LanguaL curation note: Do not confuse with *RED PEPPER*. - red bell pepper plant - - - - - - - - - - Ripe fruit of yellow bell pepper varieties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2631 - yellow bell pepper plant - - - - - - - - - - Grouped together because of similar use. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2633 - paprika, hot - red pepper (pungent pepper variety) - pungent pepper variety plant - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B3357 - LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. - plant according to family - - - - - - - - - - *Allium* is a genus of monocotyledonous flowering plants that includes hundreds of species, including the cultivated onion, garlic, scallion, shallot, leek, and chives. [https://en.wikipedia.org/wiki/Allium] - http://langual.org - http://eol.org/pages/8187 - http://www.langual.org/langual_thesaurus.asp?termid=B4302 - allium - onion - wild onion - allium species - - - - - - - - - - The biological subfamily *Bovinae* includes a diverse group of 10 genera of medium- to large-sized ungulates, including domestic cattle, the bison, African buffalo, the water buffalo, the yak, and the four-horned and spiral-horned antelopes. The evolutionary relationship between the members of the group is obscure, and their classification into loose tribes rather than formal subgroups reflects this uncertainty. General characteristics include cloven hoofs and usually at least one of the sexes of a species having true horns. - WIKIPEDIA:Bovinae - http://langual.org - http://eol.org/pages/2851454 - http://www.langual.org/langual_thesaurus.asp?termid=B4374 - bovinae - bovine - - - - - - - - - - A bovid (family *Bovidae*) is any of almost 140 species of cloven-hoofed, ruminant mammal which has males with characteristic unbranching horns covered in a permanent sheath of keratin. - -The family is widespread, being native to Asia, Africa, Europe and North America, and diverse: members include bison, African buffalo, water buffalo, antelopes, gazelles, sheep, goats, muskoxen, and domestic cattle. - WIKIPEDIA:Bovidae - http://langual.org - http://eol.org/pages/7687 - http://www.langual.org/langual_thesaurus.asp?termid=B4381 - bovidae - bovid - - - - - - - - - - The *Solanaceae*, or nightshades, are an economically important family of flowering plants. Many members of the family contain potent alkaloids, and some are highly toxic, but many, including tomatoes, potatoes, eggplant, bell/chili peppers, and tobacco are widely used. The *Solanaceae* consists of about 98 genera and some 2,700 species, with a great diversity of habitats, morphology and ecology. [https://en.wikipedia.org/wiki/Solanaceae] - http://langual.org - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B4934 - nightshade family - solanaceae plant - - - - - - - - - - *Solanum* is a large and diverse genus of flowering plants, which include two food crops of high economic importance, the potato and the tomato. It also contains the nightshades and horse nettles, as well as numerous plants cultivated for their ornamental flowers and fruit. - *Solanum* species show a wide range of growing habits, such as annual and perennials, vines, subshrubs, shrubs, and small trees. Many formerly independent genera like *Lycopersicon* (the tomatoes) and *Cyphomandra* are now included in *Solanum* as subgenera or sections. Thus, the genus today contains roughly 1,500-2,000 species. - - http://langual.org - GRIN:300568 - PLANTS:SOLAN - http://eol.org/pages/4437 - http://www.langual.org/langual_thesaurus.asp?termid=B5104 - Solanum - Solanum L. - Solanum spp. - solanum plant - - - - - - - - - - Anatomical part of the plant or animal from which a food product or its major ingredient is derived. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0116 - LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." - part of organism - - - - - - - - - - Bone, feathers, shell, skin or trim fat. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0122 - LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. - nonmeat part of animal - - - - - - - - - - Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0127 - LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. - animal body or body part - - - - - - - - - - The parts of a plant that are not fruit or seed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0148 - flower, root, stem or leaf - leaf, flower, root or stem - stem, leaf, flower or root - root, stem, leaf or flower - - - - - - - - - - Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0164 - part of animal - - - - - - - - - - - - - - - - - - - - - - The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0167 - berry - berry or fruit (anatomical part) - fruit or berry, peel undetermined - hip (fruit) - infructescence - LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. - -Renamed from *FRUIT OR BERRY* in LanguaL 2008. - fruit part - - - - - - - - - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0238 - bulb, root or tuber - tuber, bulb or root - root, tuber or bulb - - - - - - - - - - - - - - - - - - - - - - - - - - - A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. - http://langual.org - SUBSET_SIREN:F5105 - http://www.langual.org/langual_thesaurus.asp?termid=E0130 - fluid - SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - - food (liquid) - - - - - - - - - data item - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - - data item - - - - - - - - - information content entity - - A generically dependent continuant that is about some thing. - PERSON: Chris Stoeckert - OBI_0000142 - - information content entity - - - - - - - - - directive information entity - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - - directive information entity - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - - curation status specification - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - - data about an ontology part - - - - - - - - - plan specification - - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - OBI Plan and Planned Process branch - OBI_0000344 - - - plan specification - - - - - - - - - - bony vertebrates - Euteleostomi - - - - - - - - - - Dipnotetrapodomorpha - - - - - - - - - - Boreoeutheria - - - - - - - - - - Mesangiospermae - - - - - - - - - - Petrosaviidae - - - - - - - - - - Pentapetalae - - - - - - - - - - eucaryotes - eukaryotes - Eukaryota - - - - - - - - - - Bovinae - - - - - - - - - - Laurasiatheria - - - - - - - - - - tetrapods - Tetrapoda - - - - - - - - - - amniotes - Amniota - - - - - - - - - - Theria - Theria <mammals> - - - - - - - - - - Chlorophyta/Embryophyta group - chlorophyte/embryophyte group - green plants - Viridiplantae - - - - - - - - - - Opisthokonta - - - - - - - - - - Bilateria - - - - - - - - - - deuterostomes - Deuterostomia - - - - - - - - - - angiosperms - flowering plants - Magnoliopsida - - - - - - - - - - Pecora - - - - - - - - - - mammals - Mammalia - - - - - - - - - - Solanales - - - - - - - - - - nightshade family - Solanaceae - - - - - - - - - - peppers - Capsicum - - - - - - - - - - - ancho pepper plant - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2550 - C annuum - Capsicum annuum - - - - - - - - - - - WIKIPEDIA:Tomato - - http://langual.org - GRIN:101442 - ITIS:521671 - ITIS:529044 - MANSFELD:6054 - http://eol.org/pages/392557 - tomato - Lycopersicon esculentum Mill. - Lycopersicon esculentum var. esculentum P. Mill. - Solanum lycopersicum L. - lycopersicon esculentum - Solanum lycopersicum - - - - - - - - - - Solanum - - - - - - - - - - Solanoideae - - - - - - - - - - monocots - monocotyledons - Liliopsida - - - - - - - - - - Zingiberales - - - - - - - - - - ginger family - Zingiberaceae - - - - - - - - - - Zingiber - - - - - - - - - - amaryllis family - Amaryllidaceae - - - - - - - - - - Allium - - - - - - - - - - - - http://langual.org - GRIN:2244 - ITIS:42720 - PLANTS:ALCE - http://eol.org/pages/8187 - onion - Allium cepa L. - pickling onion - allium cepa - Allium cepa - - - - - - - - - - - - - Garlic (*Allium sativum*) is a species in the onion genus, *Allium*.Its close relatives include the onion, shallot, leek, chive, and Chinese onion. Garlic is native to Central Asia and northeastern Iran, and has long been a common seasoning worldwide, with a history of several thousand years of human consumption and use. [https://en.wikipedia.org/wiki/Garlic] - garlic plant - - http://langual.org - GRIN:2368 - GRIN:315611 - ITIS:42652 - MANSFELD:212 - PLANTS:ALSA2 - http://eol.org/pages/1084926 - http://www.langual.org/langual_thesaurus.asp?termid=B1233 - garlic - Allium sativum L. - allium sativum - Allium sativum - - - - - - - - - - commelinids - - - - - - - - - - vascular plants - Tracheophyta - - - - - - - - - - seed plants - Spermatophyta - - - - - - - - - - Eumetazoa - - - - - - - - - - Asteridae - asterids - - - - - - - - - - Asparagales - - - - - - - - - - chordates - Chordata - - - - - - - - - - Vertebrata - vertebrates - Vertebrata <vertebrates> - - - - - - - - - - Gnathostomata - jawed vertebrates - Gnathostomata <vertebrates> - - - - - - - - - - euphyllophytes - Euphyllophyta - - - - - - - - - - whales, hippos, ruminants, pigs, camels etc. - Artiodactyla - - - - - - - - - - lamiids - - - - - - - - - - eutherian mammals - placental mammals - placentals - Eutheria - - - - - - - - - - ginger - Zingiber officinale - - - - - - - - - - Bovidae - - - - - - - - - - oxen, cattle - Bos - - - - - - - - - - Cattle (colloquially cows) are the most common type of large domesticated ungulates. They are a prominent modern member of the subfamily *Bovinae*, are the most widespread species of the genus *Bos*, and are most commonly classified collectively as *Bos taurus*... with three subspecies: *Bos taurus primigenius, Bos taurus indicus, Bos taurus taurus*. - cattle - - - - - ITIS:183838 - MSW3:14200687 - Bos taurus Linnaeus, 1758 - bovine - cattle - cow - dairy cow - domestic cattle - domestic cow - ox - oxen - Bos taurus - - - - - - - - - - organism - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - WEB: http://en.wikipedia.org/wiki/Organism - - organism - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - - quality - - - - - - - - - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. - - quality of a liquid - - - - - - - - - A quality inhering in a bearer by virtue of its constitution. - - quality of a substance - - - - - - - - - - A plant structure (PO:0005679) which is a whole organism. - - genet (broad) - ramet (broad) - - PO_GIT:538 - PO_GIT:69 - planta entera (Spanish, exact) - 植物体全体 (Japanese, exact) - bush (narrow) - frutex (narrow) - frutices (narrow) - gametophyte (narrow) - herb (narrow) - liana (narrow) - prothalli (narrow) - prothallium (narrow) - prothallus (narrow) - seedling (narrow) - shrub (narrow) - sporophyte (narrow) - suffrutex (narrow) - suffrutices (narrow) - tree (narrow) - vine (narrow) - woody clump (narrow) - plant_anatomy - clonal colony (related) - colony (related) - PO:0000003 - - - Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). - whole plant - - - - - - - - - A floral structure primordium (PO:0025477) that is committed to the development of a gynoecium (PO:0009062). - - PO_GIT:465 - pistil primordium (exact) - portion of gynoecium primordium tissue (exact) - primordio de gineceo (Spanish, exact) - 雌蕊原基(可視的） (Japanese, exact) - plant_anatomy - PO:0000019 - Use carpel primordium (PO:0004703) for the primordium (PO:0025127) of an individual carpel (PO:0009030). - gynoecium primordium - - - - - - - - - A shoot axis (PO:0025029) that is the most distal part of a shoot system (PO:0009006) and has as parts a shoot apical meristem (PO:0020148) and the youngest primordia (PO:0025127). - - PO_GIT:234 - &#225pice del epiblasto (epiblastema) (Spanish, exact) - シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0000037 - - shoot axis apex - - - - - - - - - A portion of reproductive shoot apical meristem tissue (PO:0008028) that gives rise to the floral organs (PO:0025395). - - PO:0006329 - PO:0006373 - PO:0006374 - PO:0025091 - floral meristem (exact) - mersitema floral (Spanish, exact) - 花芽分裂組織 (Japanese, exact) - Poaceae floret meristem (narrow) - ear floret meristem (narrow) - floret meristem (narrow) - tassel floret meristem (narrow) - plant_anatomy - floral apical meristem (related) - PO:0000229 - In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). - flower meristem - - - - - - - - - A native plant cell (PO:0025606) synthesizing protoplasm and producing new cells by division and with only a primary cell wall. - - CL:0000034 - PO_GIT:272 - c&#233lula meristem&#225tica (Spanish, exact) - stem cell (exact) - 分裂組織細胞 (Japanese, exact) - plant_anatomy - PO:0004010 - - meristematic cell - - - - - - - - - - - - - - - A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) and is committed to the development of a root (PO:0009005). - - PO_GIT:467 - portion of root primordium tissue (exact) - primordio de ra&#237z (Spanish, exact) - root primordia (exact, plural) - 根原基（可視的） (Japanese, exact) - plant_anatomy - PO:0005029 - A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). - root primordium - - - - - - - - - - - - - - - A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006). - - PO_GIT:472 - PO_GIT:583 - meristema del epiblasto (epiblastema) (Spanish, exact) - シュート分裂組織 (Japanese, exact) - plant_anatomy - PO:0006079 - - shoot system meristem - - - - - - - - - A portion of meristem tissue (PO:0009013) that is the outer layer of an apical meristem (PO:0020144), or the outer layer of a plant embryo proper (PO:0000001), and gives rise to a portion of epidermis (PO:0005679). - - PO_GIT:125 - portion of protoderm tissue (exact) - protodermis (Spanish, exact) - 前表皮、原表皮 (Japanese, exact) - plant_anatomy - dermatogen cell (related) - PO:0006210 - A protoderm may or may not arise from independent initial cells (PO:0004011). Some researchers also refer to it as an epidermis in a meristematic state. - protoderm - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a whole plant (PO:0000003). - - PO_GIT:390 - plant_structure_development_stage - Solanaceae whole plant growth stages (SGN:0000001) (related) - cereal plant growth stage ontology (GRO:0007199) (related) - maize growth stage (GRO:0007002) (related) - plant growth stages in Arabidopsis (TAIR:0000021) (related) - rice growth stage (GRO:0007040) (related) - sorghum growth stage (GRO:0007124) (related) - wheat, barley and oat growth stage (GRO:0007156) (related) - PO:0007033 - - whole plant development stage - - - - - - - - - - - - - - - A shoot apical meristem (PO:0020148) that gives rise to the apical growth of reproductive tissues and organs. - - PO_GIT:36 - meristema apical reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂端 分裂組織 (Japanese, exact) - plant_anatomy - PO:0008028 - reproductive shoot apical meristem - - - - - - - - - - - - - - - A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). - - PO:0020067 - PO:0020068 - PO:0020069 - PO:0020070 - PO:0020071 - PO:0020072 - PO:0020073 - PO:0020074 - PO:0020076 - PO:0020077 - PO:0020078 - PO:0020079 - PO:0020080 - PO:0020082 - PO:0020083 - PO:0020087 - PO:0020107 - aggregate fruit (broad) - compound fruit (broad) - dehiscent fruit (broad) - diaspore (broad) - indehiscent fruit (broad) - multiple fruit (broad) - propagule (broad) - PO_GIT:76 - frucht (exact, German) - fruto (exact, Spanish) - 果実 (exact, Japanese) - coenocarp (narrow) - syncarp (narrow) - plant_anatomy - PO:0009001 - - - - - - - A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. - fruit - https://en.wikipedia.org/wiki/Fruit_anatomy - - - - - - - - - A cell which is a plant structure (PO:0009011). - - cell (broad) - GO:0005623 - PO_GIT:56 - c&#233lula vegetal (Spanish, exact) - 植物細胞 (Japanese, exact) - plant_anatomy - PO:0009002 - - - - Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. - plant cell - - - - - - - - - - - - - - - - - - - - - A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. - - PO:0003006 - PO_GIT:578 - ra&#237z (Spanish, exact) - radices (exact, plural) - radix (exact) - 根 (Japanese, exact) - aerial root (narrow) - climbing root (narrow) - plant_anatomy - PO:0009005 - - - - - - - - - - Roots function in the absorption of water and inorganic nutrients, anchoring the plant body to the substrate and supporting it, storage of food and nutrients, and vegetative reproduction. The roots of most vascular plant species enter into symbiosis with soil-borne microorganisms. Roots are usually positively geotropic and found underground, although there are many exceptions such as the aerial roots of orchids. Roots often form secondary thickening from the root lateral meristem (PO:0006308). Commonly thought of as one of the three basic parts of the plant body, along with the shoot axis (PO:0025029) and leaves (PO:0025034). - root - - - - - - - - - A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. - - PO_GIT:135 - sistema de epiblasto (epiblastema) (Spanish, exact) - シュート系、苗条系 (Japanese, exact) - tree crown (narrow) - plant_anatomy - Poaceae crown (related) - shoot (related) - thalli (related) - thallus (related) - PO:0009006 - - - The shoot system is generally used to refer to the above-ground plant parts, although some plants have parts of their shoot system underground. For example, a rhizome (PO:0004542), bulb (PO:0025356), a corm (PO:0025355) or a subterranean tuber (PO:0004547), as in Solanum tuberosum (potato) or yam, are all part of the shoot system. - shoot system - - - - - - - - - A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. - - portion of tissue (broad) - tissue (broad) - PO_GIT:59 - porci&#243n de un tejido vegetal (Spanish, exact) - 植物組織の一部 (Japanese, exact) - plant_anatomy - plant tissue (related) - PO:0009007 - - - A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. - portion of plant tissue - - - - - - - - - A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. - - organ (broad) - PO_GIT:55 - &#243rgano vegetal (Spanish, exact) - 植物 器官 (Japanese, exact) - plant_anatomy - compound plant organ (related) - simple plant organ (related) - PO:0009008 - - Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). - plant organ - - - - - - - - - - A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. - - - PO_GIT:57 - estructura vegetal (Spanish, exact) - 植物 構造 (Japanese, exact) - plant_anatomy - PO:0009011 - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - plant structure - - - - - - - - - A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. - - PO:0007021 - PO_GIT:185 - etapa de desarrollo de estructura vegetal (Spanish, exact) - plant growth and development stage (exact) - plant_structure_development_stage - Arabidopsis growth (related) - PO:0009012 - - Refers to GO:0032502 'developmental process', which includes growth, differentiation, and senescence, and BFO:0000003 'ocurrent'. - plant structure development stage - - - - - - - - - - - - - - - A portion of plant tissue (PO:0009007) in which plant cells (PO:0009002) have retained their embryonic characteristics, or have reverted to them secondarily, and that divide to produce new cells that can undergo differentiation to form mature tissues, i.e. they have a capacity for morphogenesis and growth. - - PO_GIT:472 - meristem (exact) - meristema (Spanish, exact) - meristematic tissue (exact) - 分裂組織 (Japanese, exact) - plant_anatomy - PO:0009013 - - portion of meristem tissue - - - - - - - - - - - - - - - A determinate reproductive shoot system (PO:0025082) that has as part at least one carpel (PO:0009030) or at least one stamen (PO:0009029) and does not contain any other determinate shoot system (PO:0009006) as a part. - - PO:0004541 - PO_GIT:160 - PO_GIT:259 - flor (Spanish, exact) - 花 (Japanese, exact) - Asteraceae floret (narrow) - basal flower (narrow) - double flower (narrow) - hermaphrodite flower (narrow) - monoclinous flower (narrow) - perfect flower (narrow) - plant_anatomy - floret (related) - PO:0009046 - - - - The characteristic reproductive structure of angiosperms. May have as part one or more petals, sepals or tepals. May contain one or more pistillode (PO:0009078), staminode (PO:0009077) or other aborted organs that don't show up in mature form. - flower - - - - - - - - - - - - - - - - - - - - - A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046). - - PO:0006317 - PO:0006357 - PO:0006365 - PO:0006384 - PO:0006391 - PO:0006394 - PO:0006403 - PO:0006404 - PO:0006423 - PO:0006424 - PO:0006425 - PO:0006426 - PO:0025089 - pistil (broad) - PO_GIT:470 - PO_GIT:71 - PO_GIT:98 - ginoecio (Spanish, exact) - gynaecium (exact) - gynoecia (exact, plural) - 雌蕊群 (Japanese, exact) - Poaceae gynoecium (narrow) - Zea gynoecium (narrow) - apocarpous gynoecium (narrow) - gynoecium of ear floret (narrow) - gynoecium of lower floret of pedicellate spikelet of ear (narrow) - gynoecium of lower floret of pedicellate spikelet of tassel (narrow) - gynoecium of lower floret of sessile spikelet of ear (narrow) - gynoecium of lower floret of sessile spikelet of tassel (narrow) - gynoecium of tassel floret (narrow) - gynoecium of upper floret of pedicellate spikelet of ear (narrow) - gynoecium of upper floret of pedicellate spikelet of tassel (narrow) - gynoecium of upper floret of sessile spikelet of ear (narrow) - gynoecium of upper floret of sessile spikelet of tassel (narrow) - syncarpous gynoecium (narrow) - plant_anatomy - PO:0009062 - - - If annotating gene expression to a gynoecium with a single carpel (PO:0009030), the annotation should go on carpel. A gynoecium with two or more carpels may be either syncarpous (carpels fused) or apopcarpous (carpels free) or the carpels may be partially fused. The word pistil is used synonymously with gynoecium for a synocarpous gynoecium, and synonymously with carpel for an apocarpous gynoecium, whether it has one or more carpels. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). - gynoecium - - - - - - - - - - - - - - - A maximal portion of meristem tissue (PO:0009013) located at a shoot apex (PO:0000037) or root tip (PO:0000025). - - promeristem (broad) - PO_GIT:579 - AM (exact) - meristema apical (Spanish, exact) - 頂端分裂組織 (Japanese, exact) - plant_anatomy - primary meristem (related) - PO:0020144 - - apical meristem - - - - - - - - - - - - - - - - A shoot system meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232). - - promeristem (broad) - PO_GIT:472 - SAM (exact) - meristema apical del epiblasto (epiblastema) (Spanish, exact) - 茎頂分裂組織 (Japanese, exact) - plant_anatomy - primary shoot meristem (related) - PO:0020148 - - shoot apical meristem - - - - - - - - - An axial plant organ (PO:0009008). - - rwalls - 2010-07-01T03:44:41Z - eje de la planta (Spanish, exact) - plant axes (exact, plural) - 植物軸（軸柱） (Japanese, exact) - plant_anatomy - PO:0025004 - - Includes roots and shoots. - plant axis - - - - - - - - - - - - - - - A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). - - rwalls - 2010-02-09T04:12:11Z - PO_GIT:63 - estructura vegetal colectiva de &#243rgano (Spanish, exact) - 集合植物器官構造 (Japanese, exact) - plant_anatomy - PO:0025007 - - Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. - collective plant organ structure - - - - - - - - - A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005). - - Laurel_Cooper - 2010-04-28T11:04:34Z - PO:0008033 - cycle (broad) - verticil (broad) - PO_GIT:90 - PO_GIT:99 - estructura colectiva del filoma (Spanish, exact) - 葉的器官が集まった構造 (Japanese, exact) - floral whorl (narrow) - whorl (narrow) - plant_anatomy - phyllome whorl (related) - PO:0025023 - - collective phyllome structure - - - - - - - - - - - - - - - A collective plant organ structure (PO:0025007) that produces root meristems (PO:0006085), the plant structures (PO:0009011) that arise from them and the parts thereof. - - rwalls - 2010-07-01T02:11:26Z - root (broad) - PO_GIT:136 - sistema de ra&#237z (Spanish, exact) - 根系 (Japanese, exact) - plant_anatomy - PO:0025025 - - Generally the below ground portion of a vascular plant. - root system - - - - - - - - - - - - - - - A plant axis (PO:0025004) that is part of a shoot system (PO:0009006). - - rwalls - 2010-07-01T03:46:35Z - caullome (exact) - eje del epiblasto (epiblastema) (Spanish, exact) - シュート軸 (Japanese, exact) - plant_anatomy - shoot (related) - PO:0025029 - - - - - - - Often bears leaves and branches. In vascular plants, has at least one node and one internode. - shoot axis - - - - - - - - - - - - - - - A shoot system (PO:0009006) in the sporophytic phase that has as part at least one sporangium (PO:0025094). - - rwalls - 2010-09-17T09:49:10Z - sistema de brote reproductivo (Spanish, exact) - 生殖シュート 系、苗条系 (Japanese, exact) - plant_anatomy - PO:0025082 - - reproductive shoot system - - - - - - - - - A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). - - rwalls - 2010-11-15T09:10:22Z - PO_GIT:186 - portion of primordial tissue (exact) - portion of primordium tissue (exact) - primordia (exact, plural) - primordio (Spanish, exact) - 原基（可視的） (Japanese, exact) - plant_anatomy - PO:0025127 - A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. - primordium - - - - - - - - - An anatomical entity that is or was part of a plant. - - rwalls - 2010-11-15T11:41:38Z - PO_GIT:224 - entidad anat&#243mica vegetal (Spanish, exact) - 植物 解剖学（形態）的実体 (Japanese, exact) - plant_anatomy - PO:0025131 - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - plant anatomical entity - - - - - - - - - A shoot apex that has as part a reproductive shoot apical meristem. - - rwalls - 2010-12-20T08:47:03Z - &#225pice reproductivo del epiblasto (epiblastema) (Spanish, exact) - 生殖シュート頂、茎頂 (Japanese, exact) - plant_anatomy - PO:0025222 - reproductive shoot apex - - - - - - - - - A maximal whole plant development stage. - - rwalls - 2011-10-19T10:54:37Z - PO_GIT:230 - vida de la planta entera (Spanish, exact) - 植物体の一生 (Japanese, exact) - plant_structure_development_stage - PO:0025337 - There are only two types of life of whole plant. Every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage. - life of whole plant stage - - - - - - - - - - - - - - - A plant structure development stage (PO:0009012) that has as primary participant a collective plant structure (PO:0025497). - - rwalls - 2011-10-19T11:12:49Z - PO_GIT:391 - etapa de desarrollo de una estructura colectiva de la planta (Spanish, exact) - 集合的植物構造の発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0025338 - Includes flower development stage (PO:0007615), corolla development stage (PO:0007604), and inflorescence development stage (PO:0001083). - collective plant organ structure development stage - - - - - - - - - A short, enlarged shoot system (PO:0009006) that has as parts a short stem (PO:0009047) in which the shoot internodes (PO:0005005) do not elongate, and one or more buds (PO:0000055) enclosed by fleshy leaves (PO:0009025) or leaf bases (PO:0020040). - - rwalls - 2011-11-16T03:39:15Z - diaspore (broad) - PO_GIT:173 - bulbo (Spanish, exact) - 球根、鱗茎 (Japanese, exact) - bulblet (narrow) - plant_anatomy - PO:0025356 - May serve as a storage and/or perennating organ. Usually underground. A bulb differs from a corm (PO:0025355) by having fleshy leaves or leaf bases. The outer leaves of a bulb are often dry and membranous, rather than fleshy. May bear adventitious roots. Examples include Alium and Tulipa. Not the same structure as a bulbil. - bulb - - - - - - - - - - - - - - - - - - - - - - - - - - A plant organ (PO:0009008) that is part of a flower (PO:0009046). - - rwalls - 2012-01-19T11:44:36Z - PO_GIT:423 - &#243rgano floral (Spanish, exact) - flower organ (exact) - 花器官 (Japanese, exact) - plant_anatomy - PO:0025395 - Includes phyllomes such as anthers and petals, as well as shoot axes such as androphores and gynophores. - floral organ - - - - - - - - - A portion of meristem tissue (PO:0009013) that is committed to the development of a root primordium (PO:0005029). - - Laurel_Cooper - 2012-02-08T01:00:56Z - PO_GIT:427 - precursor de ra&#237 (Spanish, exact) - 根原基 (Japanese, exact) - plant_anatomy - PO:0025433 - Only detectable by gene expression, not morphology. May arise in a pericycle (PO:0006203), as for lateral roots in most seed plants, an endodermis (PO:0000252), as for lateral roots in ferns, or from parenchyma cells (PO:0000074) that are part a shoot axis (PO:0025029), in the case of a basal root (PO:0025002) or shoot-borne root (PO:0000042). - root anlagen - - - - - - - - - - - - - - - A primordium (PO:0025127) that is committed to the development of a floral organ (PO:0025395) and is part of a reproductive shoot apex (PO:0025222). - - rwalls - 2012-04-26T03:57:09Z - PO_GIT:465 - floral structure primordia (exact, plural) - portion of floral structure primordium tissue (exact) - primordio de organo floral (Spanish, exact) - 花器官原基 (Japanese, exact) - plant_anatomy - PO:0025477 - - If annotating to a primordium of a floral structure, it is better to use the more specific term, such as petal primordium (PO:0000021) or anther primordium (PO:0006089). - floral organ primordium - - - - - - - - - A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. - - Laurel_Cooper - 2012-06-11T14:57:00Z - PO_GIT:480 - estructura vegetal con m&#250ltiples tejidos (Spanish, exact) - 複数の組織からなる植物構造 (Japanese, exact) - plant_anatomy - PO:0025496 - Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. - multi-tissue plant structure - - - - - - - - - A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). - - Laurel_Cooper - 2012-06-11T15:09:20Z - PO_GIT:479 - estructura vegetal colectiva (Spanish, exact) - 集合的植物構造 (Japanese, exact) - plant_anatomy - PO:0025497 - This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). - collective plant structure - - - - - - - - - - - - - - - A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death. - - Laurel_Cooper - 2012-12-13T18:21:19Z - PO_GIT:517 - plant_structure_development_stage - PO:0025527 - The shoot system (PO:0009006) develops fron the shoot apical meristem (PO:0020148) in the plant embryo (PO:0009009) in vascular plants. In lower plants the gametophore (PO:0030018) arises from a gametophore meristematic apical cell (PO:0030019) in the protonema (PO:0030003). - shoot system development stage - - - - - - - - - A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082). - - Laurel_Cooper - 2012-12-13T19:01:14Z - PO_GIT:517 - plant_structure_development_stage - PO:0025530 - reproductive shoot system development stage - - - - - - - - - A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in natura' (i.e. part of a natural environment). - - Laurel_Cooper - 2014-05-13T16:51:47Z - PO_GIT:586 - plant_anatomy - PO:0025606 - A native plant cell is one that is not grown or maintained in vitro, nor part of an in vitro plant structure (PO:0000004). - native plant cell - - - - - - - - - - - - - - - A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between fertilization (or apogamy) and death. - - rwalls - 2010-07-15T02:56:11Z - PO_GIT:139 - PO_GIT:68 - fase esporof&#237tica (Spanish, exact) - sporophytic development stage (exact) - sporophytic phase (exact) - sporphyte phase (exact) - 胞子体発生過程 (Japanese, exact) - plant_structure_development_stage - PO:0028002 - - A whole plant (PO:0000003) in the sporophyte development stage usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts). During the sporophyte development stage, a plant may produce meiospores by meiosis. - sporophyte development stage - - - - - - - - - A fruit (PO:0009001) which at maturity comprises a fleshy endocarp (PO:0009086), fleshy mesocarp (PO:0009087), and fleshy exocarp (PO:0009085). - - indehiscent fruit (broad) - PO_GIT:652 - bacca (exact) - baya (exact, Spanish) - beere (exact, German) - berry (exact) - pyrine (narrow) - plant_anatomy - PO:0030108 - Examples: pepper (Capsicum annuum), papaya (Carica papaya), avocado (Persea americana), may apple (Podophyllum peltatum), date palm (Phoenix dactylifera), tomato (Solanum lycopersicum), potato (Solanum tuberosum), chocolate (Theobroma cacao), blueberry (Vaccinium spp.), and grape (Vitis vinifera). - berry fruit - - - - - - - - - - - - - - - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance - - - - - - - - - Anatomical structure that is an individual member of a species and consists of more than one cell. - - multi-cellular organism - multicellular organism - - - - - - - - - A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. - - glandula mammaria - lactiferous gland - mammary gland - - - - - - - - - - - - - - - - An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0235 - mammal milk - mammary gland milk - LanguaL curation note: See scope note for *MILK OR MILK COMPONENT*. for lowfat milk use *FAT PARTIALLY REMOVED*; for skim milk, use *FAT FULLY REMOVED* (both found in D3. TREATMENT APPLIED). - milk - - - - - - - - - Gonochoristic organism that can produce female gametes. - - female organism - - - - - - - - - Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - - fluid - body fluid - bodily fluid - - - - - - - - - A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. - - adults - adult organism - - - - - - - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - group:OBI - requires discussion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tests/output/test-output.html b/tests/output/test-output.html deleted file mode 100644 index 07bb61c22..000000000 --- a/tests/output/test-output.html +++ /dev/null @@ -1,795 +0,0 @@ -

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

-

Input

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

Results

-
-

url

-N/A -

label

-Simple Spaghetti -

description

-An easy to make and delicious spaghetti dish. -

categories

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

ingredients

- -

steps

-
    -
  • item: 1:
    • -
    -
      -
    • action:
      • -AUTO:melt%3B%20saut%C3%A9 -
    • inputs:
      • - -
    • outputs:
      • -
        -
      -
    • utensils:
      • -
        -
      • item: 1:
        • -AUTO:pan -
      -
        -
    -
  • item: 2:
    • -
    -
      -
    • action:
      • -AUTO:add%3B%20cook -
    • inputs:
      • -
        -
      • item: 1:
        • -
        -
        -
      -
    • outputs:
      • -
        -
      • item: 1:
        • -
        -
          -
        • food:
          • -AUTO:meat -
        • state:
          • -well done -
            -
        -
      -
    • utensils:
      • -
        -
      • item: 1:
        • -AUTO:pan -
      -
        -
    -
  • item: 3:
    • -
    -
      -
    • action:
      • -AUTO:add%3B -
    • inputs:
      • -
        -
      • item: 1:
        • -
        -
        -
      • item: 2:
        • -
        -
          -
        • food:
          • -AUTO:salt -
        • state:
          • -None -
            -
        -
      • item: 3:
        • -
        -
        -
      • item: 4:
        • -
        -
        -
      -
    • outputs:
      • -
        -
      • item: 1:
        • -
        -
          -
        • food:
          • -AUTO:none -
        • state:
          • -None -
            -
        -
      -
    • utensils:
      • -
        -
      • item: 1:
        • -AUTO:none -
      -
        -
    -
  • item: 4:
    • -
    -
      -
    • action:
      • -AUTO:adjust -
    • inputs:
      • -
        -
      • item: 1:
        • -
        -
          -
        • food:
          • -AUTO:salt -
        • state:
          • -None -
            -
        -
      • item: 2:
        • -
        -
        -
      • item: 3:
        • -
        -
        -
      -
    • outputs:
      • -
        -
      • item: 1:
        • -
        -
          -
        • food:
          • -AUTO:inputs -
        • state:
          • -adjusted -
            -
        -
      -
    • utensils:
      • -
        -
      • item: 1:
        • -AUTO:none -
      -
        -
    -
  • item: 5:
    • -
    -
      -
    • action:
      • -AUTO:Cook -
    • inputs:
      • - -
    • outputs:
      • -
        -
      • item: 1:
        • -
        -
          -
        • food:
          • -AUTO:as%20directed -
        • state:
          • -None -
            -
        -
      -
    • utensils:
      • -
        -
      -
        -
    -
  • item: 6:
    • -
    -
      -
    • action:
      • -AUTO:mix%3B -
    • inputs:
      • - -
    • outputs:
      • - -
    • utensils:
      • -
        -
      • item: 1:
        • -AUTO:none -
      -
        -
    -
-
-

YAML Object

-
-
-extracted_object:
-  categories:
-  - AUTO:Main%20dishes
-  - AUTO:Italian%20recipes
-  description: An easy to make and delicious spaghetti dish.
-  ingredients:
-  - amount:
-      unit: AUTO:%28chopped%29
-      value: '1'
-    food_item:
-      food: AUTO:small%20onion
-      state: chopped
-  - amount:
-      unit: AUTO:%28chopped%29
-      value: '1'
-    food_item:
-      food: FOODON:00003485
-      state: chopped
-  - amount:
-      unit: UO:0010042
-      value: '2'
-    food_item:
-      food: FOODON:00003582
-      state: powder
-  - amount:
-      unit: UO:0010042
-      value: '3'
-    food_item:
-      food: FOODON:03310351
-      state: null
-  - amount:
-      unit: UO:0010040
-      value: '1'
-    food_item:
-      food: AUTO:salt
-      state: null
-  - amount:
-      unit: UO:0010040
-      value: '1'
-    food_item:
-      food: FOODON:00001649
-      state: null
-  - amount:
-      unit: null
-      value: '2'
-    food_item:
-      food: FOODON:03301217
-      state: canned
-  - amount:
-      unit: null
-      value: '1'
-    food_item:
-      food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles
-      state: uncooked
-  - amount:
-      unit: AUTO:lb
-      value: "1 - 1 1\u20442"
-    food_item:
-      food: FOODON:00001282
-      state: chopped/diced
-  label: Simple Spaghetti
-  steps:
-  - action: AUTO:melt%3B%20saut%C3%A9
-    inputs:
-    - food: FOODON:03310351
-      state: null
-    - food: FOODON:03301704
-      state: null
-    - food: FOODON:00003485
-      state: chopped
-    outputs: []
-    utensils:
-    - AUTO:pan
-  - action: AUTO:add%3B%20cook
-    inputs:
-    - food: FOODON:00001282
-      state: chopped/diced
-    outputs:
-    - food: AUTO:meat
-      state: well done
-    utensils:
-    - AUTO:pan
-  - action: AUTO:add%3B
-    inputs:
-    - food: FOODON:03000227
-      state: sauce
-    - food: AUTO:salt
-      state: null
-    - food: FOODON:00001649
-      state: null
-    - food: FOODON:00003582
-      state: powder
-    outputs:
-    - food: AUTO:none
-      state: null
-    utensils:
-    - AUTO:none
-  - action: AUTO:adjust
-    inputs:
-    - food: AUTO:salt
-      state: null
-    - food: FOODON:00001649
-      state: null
-    - food: FOODON:00003582
-      state: powder
-    outputs:
-    - food: AUTO:inputs
-      state: adjusted
-    utensils:
-    - AUTO:none
-  - action: AUTO:Cook
-    inputs:
-    - food: FOODON:03306944
-      state: null
-    outputs:
-    - food: AUTO:as%20directed
-      state: null
-    utensils: []
-  - action: AUTO:mix%3B
-    inputs:
-    - food: FOODON:03311146
-      state: null
-    - food: FOODON:03306944
-      state: null
-    outputs:
-    - food: FOODON:03306944
-      state: +
-    utensils:
-    - AUTO:none
-  url: N/A
-input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt
-input_text: "SIMPLE SPAGHETTI\n\nDIRECTIONS\nOn medium heat melt the butter and sautee\
-  \ the onion and bell peppers.\nAdd the hamburger meat and cook until meat is well\
-  \ done.\nAdd the tomato sauce, salt, pepper and garlic powder.\nSalt, pepper and\
-  \ garlic powder can be adjusted to your own tastes.\nCook noodles as directed.\n\
-  Mix the sauce and noodles if you like, I keep them separated.\n\nINGREDIENTS\nUNITS:\
-  \ US\n1\nsmall onion (chopped)\n1\nbell pepper (chopped)\n2\ntablespoons garlic\
-  \ powder\n3\ntablespoons butter\n1\nteaspoon salt\n1\nteaspoon pepper\n2\n(15 ounce)\
-  \ cans tomato sauce\n1\n(16 ounce) box spaghetti noodles\n1 - 1 1\u20442\nlb hamburger\
-  \ meat.\n"
-input_title: null
-named_entities:
-- id: FOODON:00003485
-  label: bell pepper
-- id: FOODON:00003582
-  label: garlic
-- id: UO:0010042
-  label: tablespoons
-- id: FOODON:03310351
-  label: butter
-- id: UO:0010042
-  label: tablespoons
-- id: UO:0010040
-  label: teaspoon
-- id: FOODON:00001649
-  label: pepper
-- id: UO:0010040
-  label: teaspoon
-- id: FOODON:03301217
-  label: tomato sauce
-- id: FOODON:00001282
-  label: hamburger meat
-- id: FOODON:03310351
-  label: butter
-- id: FOODON:03301704
-  label: onion
-- id: FOODON:00003485
-  label: bell peppers
-- id: FOODON:00001282
-  label: hamburger meat
-- id: FOODON:03000227
-  label: tomato
-- id: FOODON:00001649
-  label: pepper
-- id: FOODON:00003582
-  label: garlic
-- id: FOODON:00001649
-  label: pepper
-- id: FOODON:00003582
-  label: garlic
-- id: FOODON:03306944
-  label: noodles
-- id: FOODON:03311146
-  label: sauce
-- id: FOODON:03306944
-  label: noodles
-- id: FOODON:03306944
-  label: noodles
-prompt: 'Split the following piece of text into fields in the following format:
-
-
-  food: <the food item>
-
-  state: <the state of the food item (e.g. chopped, diced)>
-
-
-
-  Text:
-
-  sauce + noodles
-
-
-  ===
-
-
-  '
-raw_completion_output: "\nurl: N/A\nlabel: Simple Spaghetti\ndescription: An easy\
-  \ to make and delicious spaghetti dish.\ncategories: Main dishes; Italian recipes\n\
-  ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic\
-  \ powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce)\
-  \ cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1\u20442 lb hamburger\
-  \ meat.\nsteps: On medium heat melt the butter and saut\xE9 the onion and bell peppers;\
-  \ Add the hamburger meat and cook until meat is well done; Add the tomato sauce,\
-  \ salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted\
-  \ to your own taste; Cook noodles as directed; Mix the sauce and noodles if you\
-  \ like, I keep them separated."
-
-
- -
-

Prompt

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

Completion

-
-
-
-url: N/A
-label: Simple Spaghetti
-description: An easy to make and delicious spaghetti dish.
-categories: Main dishes; Italian recipes
-ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce) cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1⁄2 lb hamburger meat.
-steps: On medium heat melt the butter and sauté the onion and bell peppers; Add the hamburger meat and cook until meat is well done; Add the tomato sauce, salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted to your own taste; Cook noodles as directed; Mix the sauce and noodles if you like, I keep them separated.
-
- -
diff --git a/tests/output/test-output.md b/tests/output/test-output.md deleted file mode 100644 index e9668ee33..000000000 --- a/tests/output/test-output.md +++ /dev/null @@ -1,704 +0,0 @@ -# /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt - -## Input - -_SIMPLE SPAGHETTI_ - -__ - -_DIRECTIONS_ - -_On medium heat melt the butter and sautee the onion and bell peppers._ - -_Add the hamburger meat and cook until meat is well done._ - -_Add the tomato sauce, salt, pepper and garlic powder._ - -_Salt, pepper and garlic powder can be adjusted to your own tastes._ - -_Cook noodles as directed._ - -_Mix the sauce and noodles if you like, I keep them separated._ - -__ - -_INGREDIENTS_ - -_UNITS: US_ - -_1_ - -_small onion (chopped)_ - -_1_ - -_bell pepper (chopped)_ - -_2_ - -_tablespoons garlic powder_ - -_3_ - -_tablespoons butter_ - -_1_ - -_teaspoon salt_ - -_1_ - -_teaspoon pepper_ - -_2_ - -_(15 ounce) cans tomato sauce_ - -_1_ - -_(16 ounce) box spaghetti noodles_ - -_1 - 1 1⁄2_ - -_lb hamburger meat._ - -__ - -## Results - - - -### url - - -- N/A - - -### label - - -- Simple Spaghetti - - -### description - - -- An easy to make and delicious spaghetti dish. - - -### categories - - -- AUTO:Main%20dishes - -- AUTO:Italian%20recipes - - -### ingredients - - -- food_item: - - food: - - AUTO:small%20onion - - - state: - - chopped - - -- amount: - - value: - - 1 - - - unit: - - AUTO:%28chopped%29 - - - -- food_item: - - food: - - bell pepper [FOODON:00003485](https://bioregistry.io/FOODON:00003485) - - - state: - - chopped - - -- amount: - - value: - - 1 - - - unit: - - AUTO:%28chopped%29 - - - -- food_item: - - food: - - garlic [FOODON:00003582](https://bioregistry.io/FOODON:00003582) - - - state: - - powder - - -- amount: - - value: - - 2 - - - unit: - - tablespoons [UO:0010042](https://bioregistry.io/UO:0010042) - - - -- food_item: - - food: - - butter [FOODON:03310351](https://bioregistry.io/FOODON:03310351) - - - state: - - None - - -- amount: - - value: - - 3 - - - unit: - - tablespoons [UO:0010042](https://bioregistry.io/UO:0010042) - - - -- food_item: - - food: - - AUTO:salt - - - state: - - None - - -- amount: - - value: - - 1 - - - unit: - - teaspoon [UO:0010040](https://bioregistry.io/UO:0010040) - - - -- food_item: - - food: - - pepper [FOODON:00001649](https://bioregistry.io/FOODON:00001649) - - - state: - - None - - -- amount: - - value: - - 1 - - - unit: - - teaspoon [UO:0010040](https://bioregistry.io/UO:0010040) - - - -- food_item: - - food: - - tomato sauce [FOODON:03301217](https://bioregistry.io/FOODON:03301217) - - - state: - - canned - - -- amount: - - value: - - 2 - - - unit: - - None - - - -- food_item: - - food: - - AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - - - state: - - uncooked - - -- amount: - - value: - - 1 - - - unit: - - None - - - -- food_item: - - food: - - hamburger meat [FOODON:00001282](https://bioregistry.io/FOODON:00001282) - - - state: - - chopped/diced - - -- amount: - - value: - - 1 - 1 1⁄2 - - - unit: - - AUTO:lb - - - - -### steps - - -- action: - - AUTO:melt%3B%20saut%C3%A9 - -- inputs: - - food: - - butter [FOODON:03310351](https://bioregistry.io/FOODON:03310351) - - - state: - - None - - - - food: - - onion [FOODON:03301704](https://bioregistry.io/FOODON:03301704) - - - state: - - None - - - - food: - - bell pepper [FOODON:00003485](https://bioregistry.io/FOODON:00003485) - - - state: - - chopped - - -- outputs: -- utensils: - - AUTO:pan - - -- action: - - AUTO:add%3B%20cook - -- inputs: - - food: - - hamburger meat [FOODON:00001282](https://bioregistry.io/FOODON:00001282) - - - state: - - chopped/diced - - -- outputs: - - food: - - AUTO:meat - - - state: - - well done - - -- utensils: - - AUTO:pan - - -- action: - - AUTO:add%3B - -- inputs: - - food: - - tomato [FOODON:03000227](https://bioregistry.io/FOODON:03000227) - - - state: - - sauce - - - - food: - - AUTO:salt - - - state: - - None - - - - food: - - pepper [FOODON:00001649](https://bioregistry.io/FOODON:00001649) - - - state: - - None - - - - food: - - garlic [FOODON:00003582](https://bioregistry.io/FOODON:00003582) - - - state: - - powder - - -- outputs: - - food: - - AUTO:none - - - state: - - None - - -- utensils: - - AUTO:none - - -- action: - - AUTO:adjust - -- inputs: - - food: - - AUTO:salt - - - state: - - None - - - - food: - - pepper [FOODON:00001649](https://bioregistry.io/FOODON:00001649) - - - state: - - None - - - - food: - - garlic [FOODON:00003582](https://bioregistry.io/FOODON:00003582) - - - state: - - powder - - -- outputs: - - food: - - AUTO:inputs - - - state: - - adjusted - - -- utensils: - - AUTO:none - - -- action: - - AUTO:Cook - -- inputs: - - food: - - noodles [FOODON:03306944](https://bioregistry.io/FOODON:03306944) - - - state: - - None - - -- outputs: - - food: - - AUTO:as%20directed - - - state: - - None - - -- utensils: - -- action: - - AUTO:mix%3B - -- inputs: - - food: - - sauce [FOODON:03311146](https://bioregistry.io/FOODON:03311146) - - - state: - - None - - - - food: - - noodles [FOODON:03306944](https://bioregistry.io/FOODON:03306944) - - - state: - - None - - -- outputs: - - food: - - noodles [FOODON:03306944](https://bioregistry.io/FOODON:03306944) - - - state: - - + - - -- utensils: - - AUTO:none - - - - -YAML: - -
-```yaml -extracted_object: - categories: - - AUTO:Main%20dishes - - AUTO:Italian%20recipes - description: An easy to make and delicious spaghetti dish. - ingredients: - - amount: - unit: AUTO:%28chopped%29 - value: '1' - food_item: - food: AUTO:small%20onion - state: chopped - - amount: - unit: AUTO:%28chopped%29 - value: '1' - food_item: - food: FOODON:00003485 - state: chopped - - amount: - unit: UO:0010042 - value: '2' - food_item: - food: FOODON:00003582 - state: powder - - amount: - unit: UO:0010042 - value: '3' - food_item: - food: FOODON:03310351 - state: null - - amount: - unit: UO:0010040 - value: '1' - food_item: - food: AUTO:salt - state: null - - amount: - unit: UO:0010040 - value: '1' - food_item: - food: FOODON:00001649 - state: null - - amount: - unit: null - value: '2' - food_item: - food: FOODON:03301217 - state: canned - - amount: - unit: null - value: '1' - food_item: - food: AUTO:1%20%2816%20ounce%29%20box%20spaghetti%20noodles - state: uncooked - - amount: - unit: AUTO:lb - value: "1 - 1 1\u20442" - food_item: - food: FOODON:00001282 - state: chopped/diced - label: Simple Spaghetti - steps: - - action: AUTO:melt%3B%20saut%C3%A9 - inputs: - - food: FOODON:03310351 - state: null - - food: FOODON:03301704 - state: null - - food: FOODON:00003485 - state: chopped - outputs: [] - utensils: - - AUTO:pan - - action: AUTO:add%3B%20cook - inputs: - - food: FOODON:00001282 - state: chopped/diced - outputs: - - food: AUTO:meat - state: well done - utensils: - - AUTO:pan - - action: AUTO:add%3B - inputs: - - food: FOODON:03000227 - state: sauce - - food: AUTO:salt - state: null - - food: FOODON:00001649 - state: null - - food: FOODON:00003582 - state: powder - outputs: - - food: AUTO:none - state: null - utensils: - - AUTO:none - - action: AUTO:adjust - inputs: - - food: AUTO:salt - state: null - - food: FOODON:00001649 - state: null - - food: FOODON:00003582 - state: powder - outputs: - - food: AUTO:inputs - state: adjusted - utensils: - - AUTO:none - - action: AUTO:Cook - inputs: - - food: FOODON:03306944 - state: null - outputs: - - food: AUTO:as%20directed - state: null - utensils: [] - - action: AUTO:mix%3B - inputs: - - food: FOODON:03311146 - state: null - - food: FOODON:03306944 - state: null - outputs: - - food: FOODON:03306944 - state: + - utensils: - - AUTO:none - url: N/A -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/recipe-spaghetti.txt -input_text: "SIMPLE SPAGHETTI\n\nDIRECTIONS\nOn medium heat melt the butter and sautee\ - \ the onion and bell peppers.\nAdd the hamburger meat and cook until meat is well\ - \ done.\nAdd the tomato sauce, salt, pepper and garlic powder.\nSalt, pepper and\ - \ garlic powder can be adjusted to your own tastes.\nCook noodles as directed.\n\ - Mix the sauce and noodles if you like, I keep them separated.\n\nINGREDIENTS\nUNITS:\ - \ US\n1\nsmall onion (chopped)\n1\nbell pepper (chopped)\n2\ntablespoons garlic\ - \ powder\n3\ntablespoons butter\n1\nteaspoon salt\n1\nteaspoon pepper\n2\n(15 ounce)\ - \ cans tomato sauce\n1\n(16 ounce) box spaghetti noodles\n1 - 1 1\u20442\nlb hamburger\ - \ meat.\n" -input_title: null -named_entities: -- id: FOODON:00003485 - label: bell pepper -- id: FOODON:00003582 - label: garlic -- id: UO:0010042 - label: tablespoons -- id: FOODON:03310351 - label: butter -- id: UO:0010042 - label: tablespoons -- id: UO:0010040 - label: teaspoon -- id: FOODON:00001649 - label: pepper -- id: UO:0010040 - label: teaspoon -- id: FOODON:03301217 - label: tomato sauce -- id: FOODON:00001282 - label: hamburger meat -- id: FOODON:03310351 - label: butter -- id: FOODON:03301704 - label: onion -- id: FOODON:00003485 - label: bell peppers -- id: FOODON:00001282 - label: hamburger meat -- id: FOODON:03000227 - label: tomato -- id: FOODON:00001649 - label: pepper -- id: FOODON:00003582 - label: garlic -- id: FOODON:00001649 - label: pepper -- id: FOODON:00003582 - label: garlic -- id: FOODON:03306944 - label: noodles -- id: FOODON:03311146 - label: sauce -- id: FOODON:03306944 - label: noodles -- id: FOODON:03306944 - label: noodles -prompt: 'Split the following piece of text into fields in the following format: - - - food: - - state: - - - - Text: - - sauce + noodles - - - === - - - ' -raw_completion_output: "\nurl: N/A\nlabel: Simple Spaghetti\ndescription: An easy\ - \ to make and delicious spaghetti dish.\ncategories: Main dishes; Italian recipes\n\ - ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic\ - \ powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce)\ - \ cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1\u20442 lb hamburger\ - \ meat.\nsteps: On medium heat melt the butter and saut\xE9 the onion and bell peppers;\ - \ Add the hamburger meat and cook until meat is well done; Add the tomato sauce,\ - \ salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted\ - \ to your own taste; Cook noodles as directed; Mix the sauce and noodles if you\ - \ like, I keep them separated." - -``` - -
- - -Prompt: - -
-``` -Split the following piece of text into fields in the following format: - -food: -state: - - -Text: -sauce + noodles - -=== - - -``` - -
- - -Completion: - -
-``` - -url: N/A -label: Simple Spaghetti -description: An easy to make and delicious spaghetti dish. -categories: Main dishes; Italian recipes -ingredients: 1 small onion (chopped); 1 bell pepper (chopped); 2 tablespoons garlic powder; 3 tablespoons butter; 1 teaspoon salt; 1 teaspoon pepper; 2 (15 ounce) cans tomato sauce; 1 (16 ounce) box spaghetti noodles; 1 - 1 1⁄2 lb hamburger meat. -steps: On medium heat melt the butter and sauté the onion and bell peppers; Add the hamburger meat and cook until meat is well done; Add the tomato sauce, salt, pepper and garlic powder; Salt, pepper and garlic powder can be adjusted to your own taste; Cook noodles as directed; Mix the sauce and noodles if you like, I keep them separated. -``` - -
diff --git a/tests/output/training-drugmechdb.yaml b/tests/output/training-drugmechdb.yaml deleted file mode 100644 index a0e1cbd63..000000000 --- a/tests/output/training-drugmechdb.yaml +++ /dev/null @@ -1,4132 +0,0 @@ -base_model: text-davinci-003 -examples: -- completion: 'disease: MESH:D000073605 - - drug: Tetracycline - - mechanism_links: Tetracycline - disrupts - ribosomal subunit; ribosomal subunit - - location of - translation; translation - in taxon - NCBITaxon:780; NCBITaxon:780 - - causes - MESH:D000073605 - - references: https://en.wikipedia.org/wiki/Tetracycline#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tetracycline passively diffuses through porin channels in the bacterial membrane - and reversibly binds to the 30S ribosomal subunit, preventing binding of tRNA - to the mRNA-ribosome complex, and thus interfering with protein synthesis. - - - === - - - disease: MESH:D000073605 - - drug: Tetracycline - - ' -- completion: 'disease: Depressive Disorder, Major - - drug: Protriptyline - - mechanism_links: Protriptyline - decreases activity of - sodium-dependent noradrenaline - transporter (human); sodium-dependent noradrenaline transporter (human) - decreases - abundance of - Norepinephrine; Norepinephrine - participates in - neuronal signal - transduction; neuronal signal transduction - negatively correlated with - Depressive - Disorder, Major' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Protriptyline acts by decreasing the reuptake of norepinephrine and serotonin - (5-HT). - - - === - - - disease: Depressive Disorder, Major - - drug: Protriptyline - - ' -- completion: 'disease: Urinary Tract Infections - - drug: Loracarbef - - mechanism_links: loracarbef - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - prevents - peptidoglycan-protein cross-linking; peptidoglycan-protein cross-linking - - contributes to - cell wall; cell wall - in taxon - Escherichia coli; Escherichia - coli - causes - Urinary Tract Infections - - references: https://go.drugbank.com/drugs/DB00447#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Loracarbef is an oral, synthetic beta-lactam antibiotic of the carbacephem class. - Chemically, carbacephems differ from cephalosporin-class antibiotics in the dihydrothiazine - ring where a methylene group has been substituted for a sulfur atom. Loracarbef - has a spectrum of activity similar to that of the second generation cephalosporins. - It is structurally identical to cefaclor except for a sulfur atom that has been - replaced by a methylene group. This change gives greater chemical stability in - solution and allows storage at room temperature. Loracarbef, like all b-lactams - and cephalosporins, inhibits penicillin binding proteins, enzymes that create - the cross-linkage of the peptidoglycan polymer. This binding leads to interference - with the formation and remodeling of the cell wall structure. - - - === - - - disease: Urinary Tract Infections - - drug: Loracarbef - - ' -- completion: 'disease: Opioid-Related Disorders - - drug: Naloxone - - mechanism_links: Naloxone - decreases activity of - delta-type opioid receptor - (human); delta-type opioid receptor (human) - negatively regulates - InterPro:IPR000276; - Naloxone - decreases activity of - mu-type opioid receptor (human); mu-type opioid - receptor (human) - negatively regulates - InterPro:IPR000276; Naloxone - decreases - activity of - kappa-type opioid receptor (human); kappa-type opioid receptor (human) - - negatively regulates - InterPro:IPR000276; InterPro:IPR000276 - decreases activity - of - InterPro:IPR000274; InterPro:IPR000274 - decreases abundance of - Cyclic - AMP; Cyclic AMP - causes - Substance Withdrawal Syndrome; Substance Withdrawal - Syndrome - correlated with - Opioid-Related Disorders - - references: https://go.drugbank.com/drugs/DB01183#mechanismofaction; DOI:10.18773/austprescr/1996.063; - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3999180/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - While the mechanism of action of naloxone is not fully understood, the preponderance - of evidence suggests that naloxone antagonizes the opioid effects by competing - for the same receptor sites, especially the mu-opioid receptor. Recently, naloxone - has been shown to bind all three opioid receptors (mu, kappa and gamma) but the - strongest binding is to the mu receptor. - - - === - - - disease: Opioid-Related Disorders - - drug: Naloxone - - ' -- completion: 'disease: Organophosphate Poisoning - - drug: Pralidoxime - - mechanism_links: pralidoxime - increases activity of - acetylcholinesterase (human); - acetylcholinesterase (human) - positively regulates - acetylcholine catabolic - process; acetylcholine catabolic process - decreases abundance of - Acetylcholine; - Acetylcholine - contributes to - positive regulation of synaptic transmission, - cholinergic; positive regulation of synaptic transmission, cholinergic - occurs - in - Organophosphate Poisoning - - references: https://go.drugbank.com/drugs/DB00733; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1420/; - https://en.wikipedia.org/wiki/Organophosphate_poisoning#Signs_and_symptoms' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Pralidoxime is an antidote to organophosphate pesticides and chemicals. Organophosphates - bind to the esteratic site of acetylcholinesterase, which results initially in - reversible inactivation of the enzyme. Acetylcholinesterase inhibition causes - acetylcholine to accumulate in synapses, producing continuous stimulation of cholinergic - fibers throughout the nervous systems. If given within 24 hours after organophosphate - exposure, pralidoxime reactivates the acetylcholinesterase by cleaving the phosphate-ester - bond formed between the organophosphate and acetylcholinesterase. - - - === - - - disease: Organophosphate Poisoning - - drug: Pralidoxime - - ' -- completion: 'disease: Wilms Tumor - - drug: Dactinomycin - - mechanism_links: Dactinomycin - negatively regulates - DNA-templated transcription; - DNA-templated transcription - precedes - translation; Dactinomycin - directly - interacts with - DNA; DNA - participates in - DNA replication; DNA replication - - positively correlated with - HP:0031377; translation - occurs in - HP:0031377; - HP:0031377 - causes - Wilms Tumor - - references: https://go.drugbank.com/drugs/DB00970; https://drugs.ncats.io/drug/1CC1JFE158' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Good evidence exists that this drug bind strongly, but reversibly, to DNA, interfering - with synthesis of RNA (prevention of RNA polymerase elongation) and, consequently, - with protein synthesis. - - - === - - - disease: Wilms Tumor - - drug: Dactinomycin - - ' -- completion: 'disease: Mevalonate Kinase Deficiency - - drug: Canakinumab - - mechanism_links: canakinumab - decreases activity of - interleukin-1 beta (human); - interleukin-1 beta (human) - positively regulates - HP:0001945; interleukin-1 - beta (human) - positively regulates - inflammatory response; HP:0001945 - manifestation - of - Mevalonate Kinase Deficiency; inflammatory response - occurs in - Mevalonate - Kinase Deficiency - - references: https://go.drugbank.com/drugs/DB06168; https://en.wikipedia.org/wiki/Mevalonate_kinase_deficiency#Treatment' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn inflammatory diseases involving Cryopyrin-Associated Periodic Syndromes\ - \ (CAPS), interleukin-1 beta (IL-1\u03B2) is excessively activated and drives\ - \ inflammation. The protein cryopyrin controls the activation of IL-1\u03B2, and\ - \ mutations in cryopyrin's gene, NLRP-3, up-regulate IL-1\u03B2 activation. Canakinumab\ - \ is a human monoclonal anti-human IL-1\u03B2 antibody of the IgG1/\u03BA isotype.\ - \ Canakinumab binds to human IL-1\u03B2 and neutralizes its inflammatory activity\ - \ by blocking its interaction with IL-1 receptors, but it does not bind IL-1\u03B1\ - \ or IL-1 receptor antagonist (IL-1ra).\n\n===\n\ndisease: Mevalonate Kinase Deficiency\n\ - drug: Canakinumab\n" -- completion: 'disease: Hypercholesterolemia - - drug: Simvastatin - - mechanism_links: Simvastatin - decreases activity of - 3-hydroxy-3-methylglutaryl-coenzyme - A reductase (human); 3-hydroxy-3-methylglutaryl-coenzyme A reductase (human) - - negatively regulates - REACT:R-HSA-191273; REACT:R-HSA-191273 - decreases abundance - of - Cholesterol; Cholesterol - contributes to - Hypercholesterolemia - - references: https://go.drugbank.com/drugs/DB00641#mechanismofaction; https://pubchem.ncbi.nlm.nih.gov/compound/Simvastatin' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nSimvastatin is a prodrug in which the 6-membered lactone ring of simvastatin\ - \ is hydrolyzed <i>in vivo</i> to generate the beta,delta-dihydroxy\ - \ acid, an active metabolite structurally similar to HMG-CoA (hydroxymethylglutaryl\ - \ CoA). Once hydrolyzed, simvastatin competes with HMG-CoA for HMG-CoA reductase,\ - \ a hepatic microsomal enzyme, which catalyzes the conversion of HMG-CoA to mevalonate,\ - \ an early rate-limiting step in cholesterol biosynthesis.[A181421] Simvastatin\ - \ acts primarily in the liver, where decreased hepatic cholesterol concentrations\ - \ stimulate the upregulation of hepatic low density lipoprotein (LDL) receptors\ - \ which increases hepatic uptake of LDL. Simvastatin also inhibits hepatic synthesis\ - \ of very low density lipoprotein (VLDL).[F4655, F4658] The overall effect is\ - \ a decrease in plasma LDL and VLDL. Statins have also been found to bind allosterically\ - \ to \u03B22 integrin function-associated antigen-1 (LFA-1), which plays an important\ - \ role in leukocyte trafficking and in T cell activation.[A181559]\n\n===\n\n\ - disease: Hypercholesterolemia\ndrug: Simvastatin\n" -- completion: 'disease: Pneumonia, Bacterial - - drug: Ceftazidime - - mechanism_links: Ceftazidime - negatively regulates - Pfam:PF00905; Pfam:PF00905 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Streptococcus pneumoniae; - Streptococcus pneumoniae - causes - Pneumonia, Bacterial - - references: https://go.drugbank.com/drugs/DB00438; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL44354/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal activity of ceftazidime results from the inhibition of cell wall - synthesis via affinity for penicillin-binding proteins (PBPs). - - - === - - - disease: Pneumonia, Bacterial - - drug: Ceftazidime - - ' -- completion: 'disease: Meningitis - - drug: Erythromycin - - mechanism_links: Erythromycin Ethylsuccinate - negatively regulates - RNA, Ribosomal, - 23S; RNA, Ribosomal, 23S - participates in - translation; translation - occurs - in - Bacteria; Bacteria - causes - Meningitis - - references: https://go.drugbank.com/drugs/DB00199#mechanism-of-action; https://www.rxlist.com/erythromycin-ethylsuccinate-drug.htm; - https://en.wikipedia.org/wiki/Meningitis' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn order to replicate, bacteria require a specific process of protein\ - \ synthesis, enabled by ribosomal proteins.[A6505] Erythromycin acts by inhibition\ - \ of protein synthesis by binding to the 23S ribosomal RNA molecule in the 50S\ - \ subunit of ribosomes in susceptible bacterial organisms. It stops bacterial\ - \ protein synthesis by inhibiting the transpeptidation/translocation step of protein\ - \ synthesis and by inhibiting the assembly of the 50S ribosomal subunit.[L7261,A14179]\ - \ This results in the control of various bacterial infections.[A174193,L7261]\ - \ The strong affinity of macrolides, including erythromycin, for bacterial ribosomes,\ - \ supports their broad\u2010spectrum antibacterial activities.[A174193]\n\n===\n\ - \ndisease: Meningitis\ndrug: Erythromycin\n" -- completion: 'disease: Staphylococcal Infections - - drug: Teicoplanin - - mechanism_links: Teicoplanin - negatively regulates - alanylalanine; alanylalanine - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - occurs in - Staphylococcus; Staphylococcus - causes - Staphylococcal Infections - - references: https://go.drugbank.com/drugs/DB06149' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Teicoplanin inhibits peptidoglycan polymerization, resulting in inhibition of - bacterial cell wall synthesis and cell death. - - - === - - - disease: Staphylococcal Infections - - drug: Teicoplanin - - ' -- completion: 'disease: Muscle Spasticity - - drug: Chlorphenesin - - mechanism_links: Chlorphenesin - causes - relaxation of muscle; relaxation of - muscle - negatively correlated with - Muscle Spasticity - - references: https://go.drugbank.com/drugs/DB14656; https://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:3643' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The mechanism of action of chlorphenesin is not well defined, and its effects - are measured mainly by subjective responses. It is known that chlorphenesin acts - in the central nervous system (CNS) rather than directly on skeletal muscle. - - - === - - - disease: Muscle Spasticity - - drug: Chlorphenesin - - ' -- completion: 'disease: Rhinitis, Allergic, Seasonal - - drug: Brompheniramine - - mechanism_links: Brompheniramine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively correlated with - Histamine; - Histamine - positively regulates - regulation of vascular permeability; regulation - of vascular permeability - correlated with - Rhinitis, Allergic, Seasonal - - references: https://go.drugbank.com/drugs/DB00835#mechanism-of-action; https://www.uniprot.org/uniprot/P35367#function; - https://en.wikipedia.org/wiki/Allergic_rhinitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Brompheniramine is an antagonist of the H1 histamine receptors with moderate antimuscarinic - actions, as with other common antihistamines such as diphenhydramine. Due to its - anticholindergic effects, brompheniramine may cause drowsiness, sedation, dry - mouth, dry throat, blurred vision, and increased heart rate. - - - === - - - disease: Rhinitis, Allergic, Seasonal - - drug: Brompheniramine - - ' -- completion: 'disease: Lennox Gastaut Syndrome - - drug: Rufinamide - - mechanism_links: rufinamide - decreases activity of - sodium channel protein type - 9 subunit alpha (human); sodium channel protein type 9 subunit alpha (human) - - positively regulates - neuronal action potential; neuronal action potential - - positively correlated with - neurotransmitter secretion; neurotransmitter secretion - - positively correlated with - HP:0032792; HP:0032792 - positively correlated - with - Lennox Gastaut Syndrome - - references: https://go.drugbank.com/drugs/DB06201#mechanism-of-action; https://en.wikipedia.org/wiki/Rufinamide; - https://pubmed.ncbi.nlm.nih.gov/30391662/; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461817/; - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7461817/; https://en.wikipedia.org/wiki/Lennox%E2%80%93Gastaut_syndrome#Seizures' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Rufinamide is a triazole derivative antiepileptic that prolongs the inactive state - of voltage gated sodium channels thus stabilizing membranes, ultimately blocking - the spread of partial seizure activity. - - - === - - - disease: Lennox Gastaut Syndrome - - drug: Rufinamide - - ' -- completion: 'disease: Dyspareunia - - drug: Dienestrol - - mechanism_links: Dienestrol - chemically similar to - Estrogens; Estrogens - increases - activity of - estrogen receptor (human); estrogen receptor (human) - positively - regulates - REACT:R-HSA-9018519; REACT:R-HSA-9018519 - negatively correlated with - - HP:0030016; HP:0030016 - manifestation of - Dyspareunia - - references: https://go.drugbank.com/drugs/DB00890' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dienestrol is a synthetic, non-steroidal estrogen. Estrogens passively diffuse - into target cells of responsive tissues, complex with the estrogen receptors, - and enter the cell''s nucleus to initiate or enhance gene transcription of protein - synthesis after binding to DNA. - - - === - - - disease: Dyspareunia - - drug: Dienestrol - - ' -- completion: 'disease: Dysentery, Bacillary - - drug: Norfloxacin - - mechanism_links: Norfloxacin - decreases activity of - PR:P0AES5; Norfloxacin - - decreases activity of - PR:P0AFI4; PR:P0AES5 - positively regulates - DNA replication; - PR:P0AFI4 - positively regulates - DNA replication; DNA replication - occurs in - - Shigella flexneri; Shigella flexneri - causes - Dysentery, Bacillary - - references: https://go.drugbank.com/drugs/DB01059#mechanism-of-action; https://www.uniprot.org/uniprot/P0AES5#function; - https://www.uniprot.org/uniprot/P0AFI4#function; https://en.wikipedia.org/wiki/Shigellosis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of Norfloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial - DNA replication, transcription, repair, and recombination. Norfloxacin is a broad-spectrum - antibiotic agent that is shown to be effective against various Gram-positive and - Gram-negative bacterial species. The fluorine atom at the 6 position increases - potency against gram-negative organisms, and the piperazine moiety at the 7 position - is responsible for anti-pseudomonal activity - - - === - - - disease: Dysentery, Bacillary - - drug: Norfloxacin - - ' -- completion: 'disease: Breast Neoplasms - - drug: Drostanolone propionate - - mechanism_links: dromostanolone propionate - increases activity of - androgen - receptor (human); androgen receptor (human) - negatively regulates - intracellular - estrogen receptor signaling pathway; intracellular estrogen receptor signaling - pathway - positively regulates - cell population proliferation; cell population - proliferation - positively correlated with - Breast Neoplasms - - references: https://go.drugbank.com/drugs/DB14655; https://en.wikipedia.org/wiki/Drostanolone_propionate; - https://en.wikipedia.org/wiki/Anabolic_steroid#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dromostanolone is a synthetic androgenic anabolic steroid and is approximately - 5 times as potent as natural methyltestosterone. Like testosterone and other androgenic - hormones, dromostanolone binds to the androgen receptor. This causes downstream - genetic transcriptional changes. This ultimately causes retention of nitrogen, - potassium, and phosphorus; increases protein anabolism; and decreases amino acid - catabolism. The antitumour activity of dromostanolone appears related to reduction - or competitive inhibition of prolactin receptors or estrogen receptors or production. - - - === - - - disease: Breast Neoplasms - - drug: Drostanolone propionate - - ' -- completion: 'disease: Sneezing - - drug: Methdilazine - - mechanism_links: methdilazine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - participates in - histamine secretion - involved in inflammatory response; histamine secretion involved in inflammatory - response - positively correlated with - Sneezing - - references: https://go.drugbank.com/drugs/DB00902' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Methdilazine binds to the histamine H<sub>1</sub> receptor. This blocks - the action of endogenous histamine, which subsequently leads to temporary relief - of the negative symptoms brought on by histamine. - - - === - - - disease: Sneezing - - drug: Methdilazine - - ' -- completion: 'disease: Hypercholesterolemia - - drug: Inositol nicotinate - - mechanism_links: Inositol Niacinate - increases activity of - hydroxycarboxylic - acid receptor 3 (human); Inositol Niacinate - increases activity of - hydroxycarboxylic - acid receptor 2 (human); hydroxycarboxylic acid receptor 3 (human) - participates - in - REACT:R-HSA-418594; hydroxycarboxylic acid receptor 2 (human) - participates - in - REACT:R-HSA-418594; REACT:R-HSA-418594 - decreases abundance of - Triglycerides; - Triglycerides - positively correlated with - low density lipoprotein triglyceride; - Triglycerides - positively correlated with - Cholesterol, LDL; Triglycerides - - positively correlated with - Lipoproteins, LDL; low density lipoprotein triglyceride - - positively correlated with - Hypercholesterolemia; Cholesterol, LDL - positively - correlated with - Hypercholesterolemia; Lipoproteins, LDL - positively correlated - with - Hypercholesterolemia - - references: https://go.drugbank.com/drugs/DB08949#mechanism-of-action; https://en.wikipedia.org/wiki/Hypercholesterolemia#Medication; - https://pubmed.ncbi.nlm.nih.gov/15083592/; https://www.sciencedirect.com/science/article/pii/B978032329738700037X; - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441126/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nInositol nicotinate and other niacins directly and noncompetitively\ - \ inhibit microsomal enzyme diacylglycerol acyltransferase 2 (DGAT2) responsible\ - \ for esterification of fatty acids to form triglycerides, resulting in decreased\ - \ triglyceride synthesis and hepatic atherogenic lipoprotein secretion. Inhibitied\ - \ triglyceride synthesis results in accelerated intracellular hepatic apo B degradation\ - \ and the decreased secretion of VLDL and LDL particles [A19555]. Niacin also\ - \ inhibits hepatic expression of beta-chain adenosine triphosphate synthase which\ - \ inhibits the removal or uptake of HDL\u2013apo A-I. It is also suggested that\ - \ niacin increases vascular endothelial cell redox state, resulting in the inhibition\ - \ of oxidative stress and vascular inflammatory genes or key cytokines involved\ - \ in atherosclerosis. It acts as a ligand on G-protein coupled receptor 109A (HCAR2/HM74A)\ - \ and 109B (HCAR3/HM74) which mediates the anti-lipolytic and lipid-lowering effects\ - \ of nicotinic acid. Niacin-mediated signalling of GPR109A expressed on adipocytes\ - \ and G(i)-mediated decrease in cAMP levels result in decreased lipolysis, fatty\ - \ acid mobilization, and triglyceride synthesis. The action of inositol nicotinate\ - \ on GPR109A expressed on skin and macrophages to cause increased prostaglandin\ - \ D2/E2 activity is thought to be less significant compared to other niacin molecules\ - \ as it involves sustained release that leads to less flushing [A19555].\n\n===\n\ - \ndisease: Hypercholesterolemia\ndrug: Inositol nicotinate\n" -- completion: 'disease: Enterobacteriaceae Infections - - drug: Ticarcillin - - mechanism_links: Ticarcillin - negatively regulates - InterPro:IPR001460; InterPro:IPR001460 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Enterobacteriaceae; Enterobacteriaceae - - causes - Enterobacteriaceae Infections - - references: https://go.drugbank.com/drugs/DB01607' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ticarcillin''s principal mechanism of action revolves around its capacity to prevent - the cross-linking of peptidoglycan during bacterial cell wall synthesis. Consequently, - when the offending bacteria attempt to undergo cell division, cell death occurs. - - - === - - - disease: Enterobacteriaceae Infections - - drug: Ticarcillin - - ' -- completion: 'disease: Hypotension - - drug: Dopamine - - mechanism_links: Dopamine - increases activity of - alpha-1A adrenergic receptor - (human); alpha-1A adrenergic receptor (human) - positively regulates - vasoconstriction; - vasoconstriction - negatively correlated with - Hypotension; Dopamine - increases - activity of - beta-1 adrenergic receptor (human); beta-1 adrenergic receptor (human) - - positively regulates - cardiac muscle contraction; cardiac muscle contraction - - negatively correlated with - Hypotension - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL59/; https://en.wikipedia.org/wiki/Dopamine#Medical_uses' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dopamine is a precursor to norepinephrine in noradrenergic nerves and is also - a neurotransmitter in certain areas of the central nervous system. Dopamine produces - positive chronotropic and inotropic effects on the myocardium, resulting in increased - heart rate and cardiac contractility. This is accomplished directly by exerting - an agonist action on beta-adrenoceptors and indirectly by causing release of norepinephrine - from storage sites in sympathetic nerve endings. In the brain, dopamine actas - as an agonist to the five dopamine receptor subtypes (D!, D2, D3, D4, D5). - - - === - - - disease: Hypotension - - drug: Dopamine - - ' -- completion: 'disease: Hypertension - - drug: Torasemide - - mechanism_links: torsemide - decreases activity of - solute carrier family 12 - member 1 (human); solute carrier family 12 member 1 (human) - positively regulates - - sodium ion transport; sodium ion transport - regulates - renal water retention; - renal water retention - positively correlated with - HP:0032263; HP:0032263 - - manifestation of - Hypertension - - references: https://go.drugbank.com/drugs/DB00214#BE0000502; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1148/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As mentioned above, torasemide is part of the loop diuretics and thus, it acts - by reducing the oxygen demand in the medullary thick ascending loop of Henle by - inhibiting the Na+/K+/Cl- pump on the luminal cell membrane surface.[A174466] - This action is obtained by the binding of torasemide to a chloride ion-binding - site of the transport molecule.[L5257] Torasemide is known to have an effect in - the renin-angiotensin-aldosterone system by inhibiting the downstream cascade - after the activation of angiotensin II. This inhibition will produce a secondary - effect marked by the reduction of the expression of aldosterone synthase, TGF-B1 - and thromboxane A2 and a reduction on the aldosterone receptor binding.[A174466, - A174472] - - - === - - - disease: Hypertension - - drug: Torasemide - - ' -- completion: 'disease: Hyperuricemia - - drug: Lesinurad - - mechanism_links: lesinurad - decreases activity of - solute carrier family 22 - member 12 (human); solute carrier family 22 member 12 (human) - negatively correlated - with - renal urate salt excretion; renal urate salt excretion - decreases activity - of - Uric Acid; lesinurad - decreases activity of - solute carrier family 22 member - 11 (human); solute carrier family 22 member 11 (human) - negatively correlated - with - renal urate salt excretion; Uric Acid - positively correlated with - Hyperuricemia - - references: https://go.drugbank.com/drugs/DB11560#BE0000879; https://en.wikipedia.org/wiki/Lesinurad#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Lesinurad inhibits the activity of uric acid transporter 1 (URAT1) and organic - anion transporter 4 (OAT4). URAT1 is a major transporter enzyme responsible for - reuptake of uric acid from the renal tubules; inhibition of URAT1 function thereby - increases excretion of uric acid. - - - === - - - disease: Hyperuricemia - - drug: Lesinurad - - ' -- completion: 'disease: Parkinson Disease, Postencephalitic - - drug: Bromocriptine - - mechanism_links: Bromocriptine - positively regulates - D(2) dopamine receptor - (human); Bromocriptine - positively regulates - D(3) dopamine receptor (human); - D(2) dopamine receptor (human) - positively correlated with - Dopamine; D(3) dopamine - receptor (human) - positively correlated with - Dopamine; Dopamine - located in - - dopaminergic cell groups; dopaminergic cell groups - located in - substantia - nigra; substantia nigra - participates in - nigrostriatal tract; nigrostriatal - tract - affected by - Parkinson Disease, Postencephalitic - - references: https://go.drugbank.com/drugs/DB01200#BE000058; https://en.wikipedia.org/wiki/Postencephalitic_parkinsonism#:~:text=the%20free%20encyclopedia-,Postencephalitic%20parkinsonism,degeneration%20leads%20to%20clinical%20parkinsonism' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The dopamine D<sub>2</sub> receptor is a 7-transmembrane G-protein - coupled receptor associated with G<sub>i</sub> proteins. In lactotrophs, - stimulation of dopamine D<sub>2</sub> receptor causes inhibition of - adenylyl cyclase, which decreases intracellular cAMP concentrations and blocks - IP3-dependent release of Ca<sup>2+</sup> from intracellular stores. - Decreases in intracellular calcium levels may also be brought about via inhibition - of calcium influx through voltage-gated calcium channels, rather than via inhibition - of adenylyl cyclase. Additionally, receptor activation blocks phosphorylation - of p42/p44 MAPK and decreases MAPK/ERK kinase phosphorylation. Inhibition of MAPK - appears to be mediated by c-Raf and B-Raf-dependent inhibition of MAPK/ERK kinase. - Dopamine-stimulated growth hormone release from the pituitary gland is mediated - by a decrease in intracellular calcium influx through voltage-gated calcium channels - rather than via adenylyl cyclase inhibition. Stimulation of dopamine D<sub>2</sub> - receptors in the nigrostriatal pathway leads to improvements in coordinated muscle - activity in those with movement disorders. - - - === - - - disease: Parkinson Disease, Postencephalitic - - drug: Bromocriptine - - ' -- completion: 'disease: Crohn Disease - - drug: Betamethasone - - mechanism_links: Betamethasone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - decreases abundance of - cytosolic - phospholipase A2 (human); cytosolic phospholipase A2 (human) - positively regulates - - inflammatory response; inflammatory response - positively correlated with - - Crohn Disease' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Glucocorticoids inhibit neutrophil apoptosis and demargination, and inhibit NF-Kappa - B and other inflammatory transcription factors.[A187463] They also inhibit phospholipase - A2, leading to decreased formation of arachidonic acid derivatives.[A187463] In - addition, glucocorticoids promote anti-inflammatory genes like interleukin-10.[A187463] - Corticosteroids like betamethasone can act through nongenomic and genomic pathways.[A31458] - The genomic pathway is slower and occurs when glucocorticoids activate glucocorticoid - receptors and initiate downstream effects that promote transcription of anti-inflammatory - genes including phosphoenolpyruvate carboxykinase (PEPCK), IL-1-receptor antagonist, - and tyrosine amino transferase (TAT).[A31458] On the other hand, the nongenomic - pathway is able to elicit a quicker response by modulating T-cell, platelet and - monocyte activity through the use of existing membrane-bound receptors and second - messengers.[A31458] - - - === - - - disease: Crohn Disease - - drug: Betamethasone - - ' -- completion: 'disease: Hypercholesterolemia - - drug: Colestipol - - mechanism_links: Colestipol - decreases abundance of - Bile Acids and Salts; Bile - Acids and Salts - derives from - Cholesterol; Cholesterol - positively correlated - with - Hypercholesterolemia; Colestipol - increases activity of - low-density - lipoprotein receptor (human); low-density lipoprotein receptor (human) - positively - regulates - low-density lipoprotein particle clearance; low-density lipoprotein - particle clearance - decreases abundance of - Lipoproteins, LDL; Lipoproteins, - LDL - positively correlated with - Hypercholesterolemia - - references: https://go.drugbank.com/drugs/DB00375#BE0004809' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Colestipol is a lipid-lowering polymer that binds with bile acids in the intestine - forming a complex that is excreted in the feces [FDA Label, F4555, F4567]. This - non-systemic action results in a continuous, partial removal of bile acids from - the enterohepatic circulation preventing their reabsorption [FDA Label, F4555, - F4567]. This increased fecal loss of bile acids due to colestipol hydrochloride - administration leads to increased oxidation of cholesterol to bile acids [FDA - Label, F4555, F4567]. This results in an increase in the number of hepatic low-density - lipoprotein (LDL) receptors, and consequently an increased uptake of LDL and a - decrease in serum/plasma beta lipoprotein or total and LDL cholesterol levels - [FDA Label, F4555, F4567]. Although hydrochloride produces an increase in the - hepatic synthesis of cholesterol in man, serum cholesterol levels fall [FDA Label, - F4555, F4567]. - - - === - - - disease: Hypercholesterolemia - - drug: Colestipol - - ' -- completion: 'disease: HIV Infections - - drug: Lopinavir - - mechanism_links: Lopinavir - negatively regulates - PR:Q72874; PR:Q72874 - negatively - correlated with - negative regulation of peptidase activity; negative regulation - of peptidase activity - decreases activity of - gag polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)); gag polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)) - participates in - virion assembly; - virion assembly - in taxon - NCBITaxon:11676; NCBITaxon:11676 - causes - HIV Infections - - references: https://go.drugbank.com/drugs/DB01601#mechanism-of-action; https://www.uniprot.org/uniprot/P04591#function; - https://pubmed.ncbi.nlm.nih.gov/23266279/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The HIV lifecycle is comprised of 3 distinct stages: assembly, involving creation - and packaging of essential viral components; budding, wherein the viral particle - crosses the host cell plasma membrane and forms a lipid envelope; and maturation, - wherein the viral particle alters its structure and becomes infectious.[A191712] - At the center of this lifecycle is the Gag polyprotein which, along with the products - of its proteolysis, coordinate these stages and function as the major structural - proteins of the virus. The HIV-1 protease enzyme, a dimeric aspartic protease, - is the enzyme responsible for cleaving the Gag polyprotein and thus plays a critical - role in many aspects of the HIV viral lifecycle.[A191712] Lopinavir is an inhibitor - of the HIV-1 protease enzyme.[L11163] Its design is based on the "peptidomimetic" - principle, wherein the molecule contains a hydroxyethylene scaffold which mimics - the normal peptide linkage (cleaved by HIV protease) but which itself cannot be - cleaved.[A191757] By preventing HIV-1 protease activity, and thus the proteolysis - of the Gag polyprotein, lopinavir results in the production of immature, non-infectious - viral particles. - - - === - - - disease: HIV Infections - - drug: Lopinavir - - ' -- completion: 'disease: Herpes Zoster - - drug: Valaciclovir - - mechanism_links: valacyclovir - has metabolite - Acyclovir; Acyclovir - negatively - regulates - PR:P09252; PR:P09252 - positively regulates - viral DNA genome replication; - viral DNA genome replication - in taxon - NCBITaxon:10335; NCBITaxon:10335 - causes - - Herpes Zoster - - references: https://go.drugbank.com/drugs/DB00577' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Valacyclovir is the L-valine ester of aciclovir. It is classified as a nucleoside - analog DNA polymerase enzyme inhibitor. Aciclovir is a purine (guanine) nucleoside - analog is a metabolite that heavily contributes to the pharmacological actions - of valacyclovir. In fact, most of valacyclovir''s activity is attributed to acyclovir - [A175885]. 3) inactivation of the viral DNA polymerase. The higher level of antiviral - activity of acyclovir against HSV compared with VZV is attributed to its more - efficient phosphorylation by viral thymidine kinase (TK). - - - === - - - disease: Herpes Zoster - - drug: Valaciclovir - - ' -- completion: 'disease: Hyperuricemia - - drug: Sulfinpyrazone - - mechanism_links: Sulfinpyrazone - decreases activity of - solute carrier family - 22 member 12 (human); solute carrier family 22 member 12 (human) - negatively - correlated with - renal urate salt excretion; renal urate salt excretion - negatively - correlated with - Hyperuricemia - - references: https://go.drugbank.com/drugs/DB01138' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Sulfinpyrazone is an oral uricosuric agent (pyrazolone derivative) used to treat - chronic or intermittent gouty arthritis. Sulfinpyrazone competitively inhibits - the reabsorption of uric acid at the proximal convoluted tubule, thereby facilitating - urinary excretion of uric acid and decreasing plasma urate concentrations. This - is likely done through inhibition of the urate anion transporter (hURAT1) as well - as the human organic anion transporter 4 (hOAT4). Sulfinpyrazone is not intended - for the treatment of acute attacks because it lacks therapeutically useful analgesic - and anti-inflammatory effects. Sulfinpyrazone and its sulfide metabolite possess - COX inhibitory effects. Sulfinpyrazone has also been shown to be a UDP-glucuronsyltransferase - inhibitor and a very potent CYP2C9 inhibitor. Sulfinpyrazone is also known to - be a cystic fibrosis transmembrane conductance regulator (CFTR) inhibitor as well - as an inhibitor of several multridrug resistance proteins (MRPs). - - - === - - - disease: Hyperuricemia - - drug: Sulfinpyrazone - - ' -- completion: 'disease: Crohn Disease - - drug: Budesonide - - mechanism_links: Budesonide - molecularly interacts with - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases abundance of - annexin A1 - (human); annexin A1 (human) - decreases activity of - InterPro:IPR001211; glucocorticoid - receptor (human) - increases abundance of - interleukin-10 (human); interleukin-10 - (human) - decreases activity of - InterPro:IPR001211; InterPro:IPR001211 - prevents - - arachidonic acid secretion; arachidonic acid secretion - negatively regulates - - leukotriene biosynthetic process; leukotriene biosynthetic process - prevents - - inflammatory response; arachidonic acid secretion - negatively regulates - prostaglandin - biosynthetic process; prostaglandin biosynthetic process - prevents - inflammatory - response; inflammatory response - correlated with - Crohn Disease - - references: https://go.drugbank.com/drugs/DB01222#mechanismofaction; https://pubchem.ncbi.nlm.nih.gov/compound/Budesonide#section=Pharmacology; - doi:10.1165/rcmb.2016-0068OC' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Crohn Disease - - drug: Budesonide - - ' -- completion: 'disease: Rhinitis, Vasomotor - - drug: Carbinoxamine - - mechanism_links: carbinoxamine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - cellular response - to histamine; cellular response to histamine - positively correlated with - Histamine; - Histamine - participates in - inflammatory response; inflammatory response - contributes - to - Rhinitis, Vasomotor - - references: https://go.drugbank.com/drugs/DB00748#mechanism-of-action; https://www.uniprot.org/uniprot/P35367#function' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Carbinoxamine competes with free histamine for binding at HA-receptor sites. This - antagonizes the effects of histamine on HA-receptors, leading to a reduction of - the negative symptoms brought on by histamine HA-receptor binding. Carbinoxamine''s - anticholinergic action appears to be due to a central antimuscarinic effect, which - also may be responsible for its antiemetic effects, although the exact mechanism - is unknown. - - - === - - - disease: Rhinitis, Vasomotor - - drug: Carbinoxamine - - ' -- completion: 'disease: Protoporphyria, Erythropoietic - - drug: Afamelanotide - - mechanism_links: afamelanotide - increases activity of - melanocyte-stimulating - hormone receptor (human); melanocyte-stimulating hormone receptor (human) - participates - in - melanocortin receptor activity; melanocortin receptor activity - positively - regulates - melanin biosynthetic process; melanin biosynthetic process - positively - correlated with - UV protection; UV protection - negatively correlated with - - HP:0000992; HP:0000992 - manifestation of - Protoporphyria, Erythropoietic - - references: https://go.drugbank.com/drugs/DB04931#BE0002447; https://en.wikipedia.org/wiki/Erythropoietic_protoporphyria' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Patients with erythropoietic porphyria (EPP) have a deficiency of ferrochelatase - (FECH), an enzyme involved in the final step of heme biosynthesis. FECH is required - to insert iron into protoporphyrin IX (PPIX) to generate heme, and a deficiency - in FECH results in accumulation of PPIX (particularly in the liver and superficial - skin vasculature). PPIX molecules are photodynamic - exposure to UV radiation - causes these molecules to form reactive oxygen species that lead to subsequent - tissue damage.[A187199] Activation of MC1R signalling by afamelanotide also instigates - other protective processes, including an increase in antioxidant activity, DNA - repair, and secretion of immunomodulatory proteins such as interleukin-10.[A187202] - - - === - - - disease: Protoporphyria, Erythropoietic - - drug: Afamelanotide - - ' -- completion: 'disease: Prostatitis - - drug: Cephalexin - - mechanism_links: Cephalexin - decreases activity of - PR:Q8DR59; PR:Q8DR59 - positively - regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic process - - in taxon - Escherichia coli; Escherichia coli - causes - Prostatitis - - references: https://go.drugbank.com/drugs/DB00567; https://en.wikipedia.org/wiki/Cefalexin#Mechanism_of_action; - https://medlineplus.gov/ency/article/000519.htm' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Cephalexin is a first generation cephalosporin antibiotic.[A179071,A179074] Cephalosporins - contain a beta lactam and dihydrothiazide.[A179071] Unlike penicillins, cephalosprins - are more resistant to the action of beta lactamase.[A179071] Cephalexin inhibits - bacterial cell wall synthesis, leading breakdown and eventualy cell death.[Label] - - - === - - - disease: Prostatitis - - drug: Cephalexin - - ' -- completion: 'disease: Candidiasis, Oral - - drug: Ketoconazole - - mechanism_links: Ketoconazole - decreases activity of - lanosterol 14-alpha demethylase - (Candida albicans SC5314); lanosterol 14-alpha demethylase (Candida albicans SC5314) - - positively regulates - ergosterol biosynthetic process; ergosterol biosynthetic - process - positively correlated with - cell wall biogenesis; cell wall biogenesis - - occurs in - Candida albicans; Candida albicans - causes - Candidiasis, Oral - - references: https://go.drugbank.com/drugs/DB01026#mechanism-of-action; https://drugs.ncats.io/substances?q=%22KETOCONAZOLE%22; - https://www.uniprot.org/uniprot/P10613#function; https://en.wikipedia.org/wiki/Oral_candidiasis' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nKetoconazole interacts with 14-&alpha;-sterol demethylase, a cytochrome\ - \ P-450 enzyme necessary for the conversion of lanosterol to ergosterol.[A181802,T116]\ - \ This results in inhibition of ergosterol synthesis and increased fungal cellular\ - \ permeability due to reduced amounts of ergosterol present in the fungal cell\ - \ membrane. This metabolic inhibition also results in accumulation of 14\u03B1\ - -methyl-3,6-diol, a toxic metabolite. The increase in membrane fluidity is also\ - \ thought to produce impairment of membrane-bound enzyme systems as components\ - \ become less closely packed.\n\n===\n\ndisease: Candidiasis, Oral\ndrug: Ketoconazole\n" -- completion: 'disease: Tennis Elbow - - drug: Triamcinolone - - mechanism_links: Triamcinolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - has phenotype - - HP:0012531; inflammatory response - positively correlated with - HP:0100261; - HP:0012531 - manifestation of - Tennis Elbow; HP:0100261 - manifestation of - - Tennis Elbow - - references: https://go.drugbank.com/drugs/DB00620#mechanism-of-action; https://www.cancer.gov/publications/dictionaries/cancer-drug/def/triamcinolone; - https://www.ncbi.nlm.nih.gov/books/NBK544309/; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Tennis_elbow' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Corticosteroids like triamcinolone inhibit phospholipase A2 on cell membranes, - preventing the breakdown of lysosomal membranes of leukocytes, which in turn prevent - the formation of arachidonic acid, which decrease expression of cyclooxygenase - and lipoxygenase, inhibiting synthesis of prostaglandins and leukotrienes.[A184463] - Anti-inflammatory activity occurs via reversal of vascular dilation and reducing - permeability, which prevents macrophage and leukocyte migration.[A184463] Triamcinolone - also inhibits nuclear factor kappa-B, which decreases the production of pro-inflammatory - signals such as interleukin-6, interleukin-8, and monocyte chemoattractant protein-1.[A184463] - - - === - - - disease: Tennis Elbow - - drug: Triamcinolone - - ' -- completion: 'disease: Esotropia - - drug: Echothiophate - - mechanism_links: Echothiophate Iodide - decreases activity of - acetylcholinesterase - (human); Echothiophate Iodide - decreases activity of - cholinesterase (human); - cholinesterase (human) - positively regulates - acetylcholinesterase activity; - acetylcholinesterase activity - decreases abundance of - Acetylcholine; acetylcholinesterase - (human) - positively regulates - acetylcholine catabolic process; acetylcholine - catabolic process - decreases abundance of - Acetylcholine; Acetylcholine - negatively - correlated with - HP:0000549; HP:0000549 - manifestation of - Esotropia - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1201341/; - https://go.drugbank.com/drugs/DB01057#BE0002180' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Echothiophate Iodide is a long-acting cholinesterase inhibitor for topical use - which enhances the effect of endogenously liberated acetylcholine in iris, ciliary - muscle, and other parasympathetically innervated structures of the eye. Echothiophate - iodide binds irreversibly to cholinesterase, and is long acting due to the slow - rate of hydrolysis by cholinesterase. It causes miosis, increase in facility of - outflow of aqueous humor, fall in intraocular pressure, and potentiation of accommodation. - - - === - - - disease: Esotropia - - drug: Echothiophate - - ' -- completion: 'disease: Gastroesophageal Reflux - - drug: Potassium bicarbonate - - mechanism_links: potassium bicarbonate - negatively regulates - Gastric Acid; - Gastric Acid - positively correlated with - Gastroesophageal Reflux - - references: https://go.drugbank.com/drugs/DB11098' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The antacid potential of potassium bicarbonate is attained by increasing the gastrointestinal - pH by neutralizing hydrochloric acid.[T144] The increase in pH results in suppression - of the action of pepsin which is the enzyme that exacerbates ulceration due to - the presence of acid.[T143] - - - === - - - disease: Gastroesophageal Reflux - - drug: Potassium bicarbonate - - ' -- completion: 'disease: Obesity - - drug: Fenfluramine - - mechanism_links: Fenfluramine - increases activity of - 5-hydroxytryptamine receptor - 1D (human); 5-hydroxytryptamine receptor 1D (human) - positively correlated with - - Serotonin; Serotonin - negatively regulates - positive regulation of appetite; - positive regulation of appetite - positively correlated with - Obesity - - references: https://go.drugbank.com/drugs/DB00574; https://pubmed.ncbi.nlm.nih.gov/2692639/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nDravet syndrome is a complex pediatric encephalopathy characterized\ - \ by recurrent pharmacoresistant seizures of variable type, delayed development,\ - \ and in many cases, impairment in speech, language, gait, and other neurocognitive\ - \ functions.[A214694, A214709, A214712, A214715] Despite substantial variation\ - \ in presentation and severity, roughly 80% of patients with Dravet syndrome have\ - \ mutations in the _SCN1A_ gene, which encodes the alpha subunit of a voltage-gated\ - \ sodium channel (Na<sub>v</sub>1.1).[A214685, A214688, A214691, A214700,\ - \ A214709, A214715] This channel is predominantly localized in inhibitory GABAergic\ - \ interneurons as well as in excitatory pyramidal neurons; it is thought that\ - \ dysfunction of neurotransmission regulation results in the seizures and other\ - \ corresponding symptoms of Dravet syndrome.[A214700, A214709] Although the exact\ - \ mechanism by which stimulation/inhibition of various receptors leads to the\ - \ observed therapeutic benefit is unclear, it is hypothesized to be two-fold.\ - \ Stimulation of 5-HT<sub>1D</sub> and 5-HT<sub>2C</sub>\ - \ may result in increased GABAergic neurotransmission, while \u03C31 receptor\ - \ antagonism may help to modulate responses to _N_-methyl-D-aspartate (NMDA).[A214700]\n\ - \n===\n\ndisease: Obesity\ndrug: Fenfluramine\n" -- completion: 'disease: Enterocolitis - - drug: Clidinium - - mechanism_links: clidinium - negatively regulates - muscarinic acetylcholine receptor - M1 (human); muscarinic acetylcholine receptor M1 (human) - positively regulates - - smooth muscle contraction; smooth muscle contraction - positively correlated - with - gastric acid secretion; smooth muscle contraction - positively correlated - with - HP:0003394; gastric acid secretion - correlated with - Enterocolitis; HP:0003394 - - correlated with - Enterocolitis - - references: https://go.drugbank.com/drugs/DB00771#mechanism-of-action; https://en.wikipedia.org/wiki/Clidinium_bromide#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Inhibits muscarinic actions of acetylcholine at postganglionic parasympathetic - neuroeffector sites primarily by inhibiting the M1 muscarinic receptors. - - - === - - - disease: Enterocolitis - - drug: Clidinium - - ' -- completion: 'disease: Common Cold - - drug: Carbinoxamine - - mechanism_links: carbinoxamine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - cellular response - to histamine; cellular response to histamine - positively correlated with - Histamine; - Histamine - participates in - inflammatory response; inflammatory response - caused - by - NCBITaxon:12058; NCBITaxon:12058 - causes - Common Cold - - references: https://go.drugbank.com/drugs/DB00748#mechanism-of-action; https://www.uniprot.org/uniprot/P35367#function' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Carbinoxamine competes with free histamine for binding at HA-receptor sites. This - antagonizes the effects of histamine on HA-receptors, leading to a reduction of - the negative symptoms brought on by histamine HA-receptor binding. Carbinoxamine''s - anticholinergic action appears to be due to a central antimuscarinic effect, which - also may be responsible for its antiemetic effects, although the exact mechanism - is unknown. - - - === - - - disease: Common Cold - - drug: Carbinoxamine - - ' -- completion: 'disease: Nausea - - drug: Triflupromazine - - mechanism_links: Triflupromazine - decreases activity of - muscarinic acetylcholine - receptor M2 (human); muscarinic acetylcholine receptor M2 (human) - located in - - upper digestive tract; upper digestive tract - decreases activity of - gastric - acid secretion; gastric acid secretion - correlated with - Nausea - - references: https://go.drugbank.com/drugs/DB00508#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Triflupromazine binds to the dopamine D1 and dopamine D2 receptors and inhibits - their activity. The mechanism of the anti-emetic effect is due predominantly to - blockage of the dopamine D2 neurotransmitter receptors in the chemoreceptor trigger - zone (CTZ) and vomiting centre. Triflupromazine blocks the neurotransmitter dopamine - and the vagus nerve in the gastrointestinal tract. Triflupromazine also binds - the muscarinic acetylcholine receptors (M1 and M2) and the tryptamine D receptors - (5HT<sub>2B</sub>). - - - === - - - disease: Nausea - - drug: Triflupromazine - - ' -- completion: 'disease: Angina Pectoris - - drug: Bepridil - - mechanism_links: Bepridil - decreases activity of - sodium/potassium-transporting - ATPase subunit alpha-1 (human); sodium/potassium-transporting ATPase subunit alpha-1 - (human) - positively regulates - sodium ion export across plasma membrane; sodium - ion export across plasma membrane - positively correlated with - calcium ion import; - calcium ion import - positively correlated with - Myocardial Ischemia; Myocardial - Ischemia - positively correlated with - Angina Pectoris - - references: https://go.drugbank.com/drugs/DB01244#BE0000732 https://www.ahajournals.org/doi/full/10.1161/01.STR.29.3.705' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Bepridil has inhibitory effects on both the slow calcium (L-type) and fast sodium - inward currents in myocardial and vascular smooth muscle, interferes with calcium - binding to calmodulin, and blocks both voltage and receptor operated calcium channels. - Bepridil inhibits the transmembrane influx of calcium ions into cardiac and vascular - smooth muscle. This has been demonstrated in isolated myocardial and vascular - smooth muscle preparations in which both the slope of the calcium dose response - curve and the maximum calcium-induced inotropic response were significantly reduced - by bepridil. In cardiac myocytes <i>in vitro</i>, bepridil was shown - to be tightly bound to actin. Bepridil regularly reduces heart rate and arterial - pressure at rest and at a given level of exercise by dilating peripheral arterioles - and reducing total peripheral resistance (afterload) against which the heart works. - - - === - - - disease: Angina Pectoris - - drug: Bepridil - - ' -- completion: 'disease: Lymphoma, Non-Hodgkin - - drug: Pixantrone - - mechanism_links: pixantrone - increases abundance of - DNA Adducts; DNA Adducts - - decreases activity of - DNA topoisomerase 2-alpha (human); DNA topoisomerase - 2-alpha (human) - positively regulates - cellular response to DNA damage stimulus; - cellular response to DNA damage stimulus - positively regulates - apoptotic chromosome - condensation; apoptotic chromosome condensation - positively correlated with - - cell death; cell death - decreases abundance of - neoplastic cell; neoplastic - cell - manifestation of - Lymphoma, Non-Hodgkin - - references: https://go.drugbank.com/drugs/DB06193; https://en.wikipedia.org/wiki/Pixantrone' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Pixantrone is an aza-anthracenedione which acts as a DNA intercalator. By intercalating - between DNA, with modest affinity, it stimulates DNA cleavage by topoisomerase - II. (Pixantrone acts as a poison to topoisomerase II by stabilizing protein-DNA - complexes which are usually transient, giving rise to double stranded DNA breaks.) - The first line agent doxorubicin is cardiotoxic, in part, due to its ability to - redox activate the superoxide anion and hydrogen peroxide, and form a long-lived - secondary alcohol metabolite: doxorubicinol. [3] Clearance of doxorubicin from - myocardial tissue is incomplete, and it can be found months or years after the - last administration. [3] In doxorubicin treated ex vivo cardiac strips, pixantrone - formed an N-dealkylated product that inhibited metabolism of residual doxorubicin - into doxorubicinol. Additionally, in ex vivo human myocardial strips (doxorubicin - naive, and doxorubicin pretreated) pixantrone showed high cardiac uptake without - formation of superoxide anion or hydrogen peroxide. Pixantrones lack of cardiotoxicity - is thus attributed to its redox inactivity and inhibition of doxorubicinol formation. - [3] - - - === - - - disease: Lymphoma, Non-Hodgkin - - drug: Pixantrone - - ' -- completion: 'disease: Dermatitis, Seborrheic - - drug: Halcinonide - - mechanism_links: Halcinonide - positively regulates - glucocorticoid receptor - (human); glucocorticoid receptor (human) - negatively correlated with - HP:0001019; - HP:0001019 - manifestation of - Dermatitis, Seborrheic - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1200845/; - https://en.wikipedia.org/wiki/Halcinonide; https://pubchem.ncbi.nlm.nih.gov/compound/443943#section=Mechanism-of-Action; - https://en.wikipedia.org/wiki/Corticosteroid#Pharmacology' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The precise mechanism of action of topical corticosteroids is unclear. However - they possess anti-inflammatory, antipruritic, and vasoconstrictive actions. New - research indicates that halcinonide activates MBP (myelin basic protein) expression - via smoothened receptor activation. This finding suggests that halcinonide could - be used in the treatment of multiple sclerosis therapy as an alternative to Dexamethasone - or Methylprednisolone. - - - === - - - disease: Dermatitis, Seborrheic - - drug: Halcinonide - - ' -- completion: 'disease: Hyperglycemia - - drug: Inulin - - mechanism_links: Inulin - positively regulates - negative regulation of appetite; - negative regulation of appetite - prevents - Hyperglycemia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a diagnostic agent, inulin is readily soluble and essentially indigestible. - It readily passes through the blood and into the urine. It is neither secreted - nor resorbed by the kidney making it an excellent indicator for renal clearance - rates. The inulin clearance test has largely been succeeded by the creatinine - clearance test as a measure of glomerular filtration rate. Inulin is a hypoglycemic - agent. Since it is not digestible by human enzymes ptyalin and amylase, inulin - passes through much of the digestive system intact. It is only in the colon that - bacteria metabolise inulin, with the release of significant quantities of carbon - dioxide and/or methane. Because inulin is not broken down into simple sugars (monosaccharides) - by normal digestion, it does not elevate blood sugar levels, hence, helping diabetics - regulate blood sugar levels. - - - === - - - disease: Hyperglycemia - - drug: Inulin - - ' -- completion: 'disease: Tinea Pedis - - drug: Benzocaine - - mechanism_links: Benzocaine - decreases activity of - sodium channel protein type - 10 subunit alpha (human); sodium channel protein type 10 subunit alpha (human) - - participates in - voltage-gated sodium channel activity; voltage-gated sodium - channel activity - increases transport of - Sodium; Sodium - positively correlated - with - membrane depolarization; membrane depolarization - positively regulates - - neuronal action potential; neuronal action potential - occurs in - pain receptor - cell; pain receptor cell - participates in - sensory perception of pain; sensory - perception of pain - occurs in - Tinea Pedis - - references: https://go.drugbank.com/drugs/DB01086; https://en.wikipedia.org/wiki/Benzocaine' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Benzocaine binds to sodium channels and reversibly stabilizes the neuronal membrane - which decreases its permeability to sodium ions. Depolarization of the neuronal - membrane is inhibited thereby blocking the initiation and conduction of nerve - impulses. - - - === - - - disease: Tinea Pedis - - drug: Benzocaine - - ' -- completion: 'disease: Depressive Disorder - - drug: Amoxapine - - mechanism_links: Amoxapine - negatively regulates - sodium-dependent serotonin - transporter (human); sodium-dependent serotonin transporter (human) - positively - regulates - serotonin uptake; serotonin uptake - positively correlated with - - Depressive Disorder - - references: https://go.drugbank.com/drugs/DB00543#mechanism-of-action; https://en.wikipedia.org/wiki/Amoxapine#Pharmacology' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Amoxapine acts by decreasing the reuptake of norepinephrine and serotonin (5-HT). - - - === - - - disease: Depressive Disorder - - drug: Amoxapine - - ' -- completion: 'disease: HIV Infections - - drug: Abacavir - - mechanism_links: abacavir - increases abundance of - carbovir triphosphate; carbovir - triphosphate - decreases activity of - gag-pol polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)); gag-pol polyprotein (human immunodeficiency - virus type 1 group M subtype B (isolate HXB2)) - participates in - viral DNA genome - replication; viral DNA genome replication - causes - HIV Infections' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nAbacavir is a carbocyclic synthetic nucleoside analogue and an antiviral\ - \ agent. Intracellularly, abacavir is converted by cellular enzymes to the active\ - \ metabolite carbovir triphosphate, an analogue of deoxyguanosine-5'-triphosphate\ - \ (dGTP). Carbovir triphosphate inhibits the activity of HIV-1 reverse transcriptase\ - \ (RT) both by competing with the natural substrate dGTP and by its incorporation\ - \ into viral DNA. Viral DNA growth is terminated because the incorporated nucleotide\ - \ lacks a 3'-OH group, which is needed to form the 5\u2032 to 3\u2032 phosphodiester\ - \ linkage essential for DNA chain elongation.\n\n===\n\ndisease: HIV Infections\n\ - drug: Abacavir\n" -- completion: 'disease: Humoral Hypercalcemia Of Malignancy - - drug: Pamidronic acid - - mechanism_links: pamidronate - decreases activity of - farnesyl pyrophosphate - synthase (human); pamidronate - decreases activity of - geranylgeranyl pyrophosphate - synthase (human); pamidronate - molecularly interacts with - hydroxylapatite; - hydroxylapatite - positively correlated with - ossification; hydroxylapatite - - positively correlated with - bone regeneration; farnesyl pyrophosphate synthase - (human) - positively correlated with - isoprenoid biosynthetic process; geranylgeranyl - pyrophosphate synthase (human) - positively correlated with - isoprenoid biosynthetic - process; isoprenoid biosynthetic process - positively regulates - osteoclast; - osteoclast - positively correlated with - bone resorption; bone resorption - positively - correlated with - Humoral Hypercalcemia Of Malignancy; ossification - negatively - correlated with - Humoral Hypercalcemia Of Malignancy; bone regeneration - negatively - correlated with - Humoral Hypercalcemia Of Malignancy - - references: https://go.drugbank.com/drugs/DB00282; https://pubchem.ncbi.nlm.nih.gov/compound/4674' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Bisphosphonates are taken into the bone where they bind to hydroxyapatite. Bone - resorption by osteoclasts causes local acidification, releasing the bisphosphonate, - which is taken into the osteoclast by fluid-phase endocytosis.[A959] Endocytic - vesicles become acidified, releasing bisphosphonates into the cytosol of osteoclasts - where they act.[A959] Nitrogen containing bisphosphonates such as pamidronate - are known to induce apoptosis of hematopoietic tumor cells by inhibiting the components - of the mevalonate pathway farnesyl diphosphate synthase, farnesyl diphosphate, - and geranylgeranyl diphosphate.[A202769,A203123,A203111] These components are - essential for post-translational prenylation of GTP-binding proteins like Rap1.[A202769,A203123] - The lack of prenylation of these proteins interferes with their function, and - in the case of Rap1, leads to apoptosis.[A202769,A203123] pamidronate also activated - caspases 3 and 9 which further contribute to apoptosis.[A202769,A203123,A203177] - - - === - - - disease: Humoral Hypercalcemia Of Malignancy - - drug: Pamidronic acid - - ' -- completion: 'disease: Stevens-Johnson Syndrome - - drug: Prednisolone - - mechanism_links: Prednisolone - increases activity of - glucocorticoid receptor - (human); glucocorticoid receptor (human) - increases activity of - annexin A1 - (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - contributes to - - HP:0008066; HP:0008066 - manifestation of - Stevens-Johnson Syndrome - - references: https://go.drugbank.com/drugs/DB00860#mechanism-of-action; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Stevens%E2%80%93Johnson_syndrome' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The short term effects of corticosteroids are decreased vasodilation and permeability - of capillaries, as well as decreased leukocyte migration to sites of inflammation.[A187463] - Corticosteroids binding to the glucocorticoid receptor mediates changes in gene - expression that lead to multiple downstream effects over hours to days.[A187463] - Lower doses of corticosteroids provide an anti-inflammatory effect, while higher - doses are immunosuppressive.[A187463] High doses of glucocorticoids for an extended - period bind to the mineralocorticoid receptor, raising sodium levels and decreasing - potassium levels.[A187463] - - - === - - - disease: Stevens-Johnson Syndrome - - drug: Prednisolone - - ' -- completion: 'disease: Carcinoma, Non-Small-Cell Lung - - drug: Vinorelbine - - mechanism_links: vinorelbine - decreases activity of - InterPro:IPR000217; InterPro:IPR000217 - - positively regulates - G2/M transition of mitotic cell cycle; G2/M transition - of mitotic cell cycle - positively correlated with - cell division; cell division - - positively correlated with - HP:0031377; HP:0031377 - positively correlated - with - Carcinoma, Non-Small-Cell Lung - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL553025/; https://go.drugbank.com/drugs/DB00361#mechanism-of-action; - https://en.wikipedia.org/wiki/Vinorelbine#Pharmacology' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Vinca alkaloids are structurally similar compounds composed of two multi-ringed - units, _vindoline_, and _catharanthine_. _Vinorelbine tartrate_ is a vinca alkaloid - in which the catharanthine component is the target of structural modification - [L2005], [L2006]. - - - === - - - disease: Carcinoma, Non-Small-Cell Lung - - drug: Vinorelbine - - ' -- completion: 'disease: Bronchial Spasm - - drug: Dyphylline - - mechanism_links: Dyphylline - decreases activity of - InterPro:IPR043371; InterPro:IPR043371 - - increases abundance of - Cyclic AMP; Cyclic AMP - causes - response to bronchodilator; - response to bronchodilator - enables - relaxation of smooth muscle; relaxation - of smooth muscle - located in - bronchus; bronchus - contributes to - vasodilation; - vasodilation - correlated with - Bronchial Spasm - - references: https://go.drugbank.com/drugs/DB00651#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bronchodilatory action of dyphylline, as with other xanthines, is thought - to be mediated through competitive inhibition of phosphodiesterase with a resulting - increase in cyclic AMP producing relaxation of bronchial smooth muscle as well - as antagonism of adenosine receptors. - - - === - - - disease: Bronchial Spasm - - drug: Dyphylline - - ' -- completion: 'disease: Urticaria - - drug: Azatadine - - mechanism_links: azatadine - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - inflammatory response - causes - Urticaria - - references: https://go.drugbank.com/drugs/DB00719; https://en.wikipedia.org/wiki/Antihistamine#H1-antihistamines; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL946/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Antihistamines such as azatadine appear to compete with histamine for histamine - H1- receptor sites on effector cells. The antihistamines antagonize those pharmacological - effects of histamine which are mediated through activation of H1- receptor sites - and thereby reduce the intensity of allergic reactions and tissue injury response - involving histamine release. - - - === - - - disease: Urticaria - - drug: Azatadine - - ' -- completion: 'disease: Heart Failure - - drug: Levosimendan - - mechanism_links: simendan - increases stability of - troponin C, slow skeletal - and cardiac muscles (human); troponin C, slow skeletal and cardiac muscles (human) - - positively regulates - heart contraction; heart contraction - negatively correlated - with - Heart Failure; simendan - increases activity of - ATP-sensitive inward - rectifier potassium channel 11 (human); simendan - increases activity of - ATP-sensitive - inward rectifier potassium channel 8 (human); ATP-sensitive inward rectifier potassium - channel 11 (human) - positively regulates - relaxation of smooth muscle; ATP-sensitive - inward rectifier potassium channel 8 (human) - positively regulates - relaxation - of smooth muscle; relaxation of smooth muscle - positively regulates - vasodilation; - vasodilation - negatively correlated with - HP:0000822; HP:0000822 - affects risk - for - Heart Failure - - references: https://go.drugbank.com/drugs/DB00922' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Levosimendan appears to increase myofilament calcium sensitivity by binding to - cardiac troponin C in a calcium-dependent manner. This stabilizes the calcium-induced - conformational change of troponin C, thereby (1) changing actin-myosin cross-bridge - kinetics apparently without increasing the cycling rate of the cross-bridges or - myocardial ATP consumption, (2) increasing the effects of calcium on cardiac myofilaments - during systole and (3) improving contraction at low energy cost (inotropic effect). - Calcium concentration and, therefore, sensitization decline during diastole, allowing - normal or improved diastolic relaxation. Levosimendan also leads to vasodilation - through the opening of ATP-sensitive potassium channels. By these inotropic and - vasodilatory actions, levosimendan increases cardiac output without increasing - myocardial oxygen demand. Levosimendan also has a selective phosphodiesterase - (PDE)-III inhibitory action that may contribute to the inotropic effect of this - compound under certain experimental conditions. It has been reported that levosimendan - may act preferentially as a Ca<sup>2+</sup> sensitizer at lower concentrations, - whereas at higher concentrations its action as a PDE-III inhibitor becomes more - prominent in experimental animals and humans. - - - === - - - disease: Heart Failure - - drug: Levosimendan - - ' -- completion: 'disease: Dacryocystitis - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:P68790; PR:P68790 - - positively regulates - translation; translation - occurs in - Staphylococcus aureus; - Staphylococcus aureus - causes - Dacryocystitis - - references: https://go.drugbank.com/drugs/DB02703#mechanism-of-action; https://en.wikipedia.org/wiki/Fusidic_acid; - https://www.uniprot.org/uniprot/P68790#function; https://en.wikipedia.org/wiki/Dacryocystitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Dacryocystitis - - drug: Fusidic acid - - ' -- completion: 'disease: Hypertension, Pulmonary - - drug: Epoprostenol - - mechanism_links: Epoprostenol - positively correlated with - prostacyclin receptor - (human); prostacyclin receptor (human) - positively regulates - prostacyclin receptor - activity; prostacyclin receptor activity - positively regulates - vasodilation; - vasodilation - negatively correlated with - HP:0032263; HP:0032263 - manifestation - of - Hypertension, Pulmonary - - references: https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1139/; https://go.drugbank.com/drugs/DB01240#BE0000475' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Prostaglandins are present in most body tissues and fluids and mediate many biological - functions. Epoprostenol (PGI2) is a member of the family of prostaglandins that - is derived from arachidonic acid. The major pharmacological actions of epoprostenol - is ultimately inhibition of platelet aggregation. Prostacycline (PGI2) from endothelial - cells activate G protein-coupled receptors on platelets and endothelial cells. - This activation causes adenylate cyclase to produce cyclic AMP which inhibits - further platelet activation and activates protein kinase A. Cyclic AMP also prevents - coagulation by preventing an increase in intracellular calcium from thromboxane - A2 binding. PKA then continues the cascade by phosphorylating and inhibiting myosin - light-chain kinase which leads to smooth muscle relaxation and vasodilation. Notably, - PGI2 and TXA2 work as physiological antagonists. - - - === - - - disease: Hypertension, Pulmonary - - drug: Epoprostenol - - ' -- completion: 'disease: Hepatic Encephalopathy - - drug: Erythromycin - - mechanism_links: Erythromycin Ethylsuccinate - negatively regulates - RNA, Ribosomal, - 23S; RNA, Ribosomal, 23S - participates in - translation; translation - occurs - in - Bacteria; Bacteria - causes - Hepatic Encephalopathy - - references: https://go.drugbank.com/drugs/DB00199#mechanism-of-action; https://www.rxlist.com/erythromycin-ethylsuccinate-drug.htm; - https://en.wikipedia.org/wiki/Hepatic_encephalopathy' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nIn order to replicate, bacteria require a specific process of protein\ - \ synthesis, enabled by ribosomal proteins.[A6505] Erythromycin acts by inhibition\ - \ of protein synthesis by binding to the 23S ribosomal RNA molecule in the 50S\ - \ subunit of ribosomes in susceptible bacterial organisms. It stops bacterial\ - \ protein synthesis by inhibiting the transpeptidation/translocation step of protein\ - \ synthesis and by inhibiting the assembly of the 50S ribosomal subunit.[L7261,A14179]\ - \ This results in the control of various bacterial infections.[A174193,L7261]\ - \ The strong affinity of macrolides, including erythromycin, for bacterial ribosomes,\ - \ supports their broad\u2010spectrum antibacterial activities.[A174193]\n\n===\n\ - \ndisease: Hepatic Encephalopathy\ndrug: Erythromycin\n" -- completion: 'disease: Chlamydial Pneumonia - - drug: Sparfloxacin - - mechanism_links: sparfloxacin - decreases activity of - PR:Q9Z7I9; sparfloxacin - - decreases activity of - PR:Q54A16; PR:Q9Z7I9 - participates in - bacterial-type - DNA replication; PR:Q54A16 - participates in - bacterial-type DNA replication; - bacterial-type DNA replication - occurs in - NCBITaxon:83558; NCBITaxon:83558 - - causes - Chlamydial Pneumonia - - references: https://go.drugbank.com/drugs/DB01208#mechanism-of-action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of sparfloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial - DNA replication, transcription, repair, and recombination. - - - === - - - disease: Chlamydial Pneumonia - - drug: Sparfloxacin - - ' -- completion: 'disease: Hypertension - - drug: Eprosartan - - mechanism_links: eprosartan - negatively regulates - type-1 angiotensin II receptor - (human); type-1 angiotensin II receptor (human) - positively correlated with - - Angiotensin II; Angiotensin II - positively regulates - Vasoconstriction; Vasoconstriction - - positively correlated with - HP:0032263; HP:0032263 - positively correlated - with - Hypertension - - references: https://go.drugbank.com/drugs/DB00876' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Eprosartan blocks the vasoconstrictor and aldosterone-secreting effects of angiotensin - II by selectively blocking the binding of angiotensin II to the AT<sub>1</sub> - receptor found in many tissues (e.g., vascular smooth muscle, adrenal gland). - There is also an AT<sub>2</sub> receptor found in many tissues but - it is not known to be associated with cardiovascular homeostasis. Eprosartan does - not exhibit any partial agonist activity at the AT<sub>1</sub> receptor. - Its affinity for the AT<sub>1</sub> receptor is 1,000 times greater - than for the AT<sub>2</sub> receptor. In vitro binding studies indicate - that eprosartan is a reversible, competitive inhibitor of the AT<sub>1</sub> - receptor. Eprosartan has also been shown to bind to AT<sub>1</sub> - receptors both presynaptically and synaptically. Its action on presynaptic AT<sub>1</sub> - receptors results in the inhibition of sympathetically stimulated noradrenaline - release. Unlike ACE inhibitors, eprosartan and other ARBs do not interfere with - response to bradykinins and substance P, which allows for the absence of adverse - effects that are present in ACE inhibitors (eg. dry cough). - - - === - - - disease: Hypertension - - drug: Eprosartan - - ' -- completion: 'disease: Tinea Pedis - - drug: Luliconazole - - mechanism_links: 4-(2,4-dichlorophenyl)-1,3-dithiolan-2-ylidene-1-imidazolylacetonitrile - - negatively regulates - InterPro:IPR001128; InterPro:IPR001128 - positively regulates - - ergosterol biosynthetic process; ergosterol biosynthetic process - in taxon - - NCBITaxon:5551; NCBITaxon:5551 - causes - Tinea Pedis - - references: https://go.drugbank.com/drugs/DB08933; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL2105689/; - https://en.wikipedia.org/wiki/Antifungal#Azoles' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The exact mechanism of action for luliconazole''s anti-fungal activity is still - not known, but luliconazole is thought to inhibit the enzyme lanosterol demethylase. - Lanosterol demethylase is needed for the synthesis of ergosterol, which is a major - component of the fungus cell membranes. - - - === - - - disease: Tinea Pedis - - drug: Luliconazole - - ' -- completion: 'disease: Adenocarcinoma, Follicular - - drug: Lenvatinib - - mechanism_links: lenvatinib - decreases activity of - platelet-derived growth - factor receptor alpha (human); platelet-derived growth factor receptor alpha (human) - - disrupts - cellular process; cellular process - located in - malignant cell; - malignant cell - participates in - Adenocarcinoma, Follicular - - references: https://go.drugbank.com/drugs/DB09078#mechanismofaction' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nLenvatinib is a receptor tyrosine kinase (RTK) inhibitor that inhibits\ - \ the kinase activities of vascular endothelial growth factor (VEGF) receptors\ - \ VEGFR1 (FLT1), VEGFR2 (KDR), and VEGFR3 (FLT4). Lenvatinib also inhibits other\ - \ RTKs that have been implicated in pathogenic angiogenesis, tumor growth, and\ - \ cancer progression in addition to their normal cellular functions, including\ - \ fibroblast growth factor (FGF) receptors FGFR1, 2, 3, and 4; the platelet derived\ - \ growth factor receptor alpha (PDGFR\u03B1), KIT, and RET.\n\n===\n\ndisease:\ - \ Adenocarcinoma, Follicular\ndrug: Lenvatinib\n" -- completion: 'disease: Constipation - - drug: Magnesium hydroxide - - mechanism_links: Magnesium Hydroxide - subclass of - Laxatives; Laxatives - positively - correlated with - defecation; defecation - negatively correlated with - Constipation - - references: https://go.drugbank.com/drugs/DB09104' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The suspension of magnesium hydroxide is ingested and enters the stomach. According - to the amount ingested, the magnesium hydroxide will either act as an antacid - or a laxative. Through the ingestion of 2-5 grams (in adults) the magnesium hydroxide - acts as a laxative in the colon. The majority of the suspension is not absorbed - in the intestinal tract and will create an osmotic effect to draw water into the - gut from surrounding tissues. With this increase of water in the intestines, the - feces will soften and the intraluminal volume of the feces will increase. These - effects still stimulate intestinal motility and induce the urge to defecate. Magnesium - hydroxide will also release cholecystokinin (CKK) in the intestines which will - accumulate water and electrolytes in the lumen and furthermore increase intestinal - motility. - - - === - - - disease: Constipation - - drug: Magnesium hydroxide - - ' -- completion: 'disease: Atrial Fibrillation - - drug: Quinidine - - mechanism_links: Quinidine - disrupts - InterPro:PR001696; InterPro:PR001696 - - positively regulates - cardiac conduction; cardiac conduction - positively correlated - with - cardiac muscle contraction; cardiac muscle contraction - positively correlated - with - Atrial Fibrillation - - references: https://pubchem.ncbi.nlm.nih.gov/compound/441074; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1294/; - https://www.drugs.com/pro/quinidine-gluconate.html#s-34090-1' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Quinidine acts on sodium channels on the neuronal cell membrane, limiting the - spread of seizure activity and reducing seizure propagation. The antiarrhythmic - actions are mediated through effects on sodium channels in Purkinje fibers. Quinidine - may also act on the slow inward calcium current (ICa), the rapid (IKr) and slow - (IKs) components of the delayed potassium rectifier current, the inward potassium - rectifier current (IKI), the ATP-sensitive potassium channel (IKATP) and Ito. - - - === - - - disease: Atrial Fibrillation - - drug: Quinidine - - ' -- completion: 'disease: Avitaminosis - - drug: Sodium fluoride - - mechanism_links: Sodium Fluoride - contraindicated for - Avitaminosis - - references: https://go.drugbank.com/drugs/DB09325; https://www.sciencedirect.com/science/article/abs/pii/S0736574815300630' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The prevention of dental caries by topical fluoride is achieved by various mechanisms.[A181703] - Sodium fluoride kills bacteria that cause caries, such a Streptococcus mutans - and lactobacilli[A181718] by interfering with their metabolic activities that - result in the formation of lactic acid. Fluoride ions cause the inhibition of - glycolytic and other enzymes involved in bacterial metabolism. It changes the - permeability of cell membranes, lowering the pH in the cytoplasm of the cell, - leading to a decrease in acidity, which is normally implicated in tooth decay.[A181652] When - administered at low topical doses, fluoride in both saliva and plaque and saliva - prevent the demineralization of healthy tooth enamel while remineralizing teeth - that have previously been demineralized. Sodium fluoride is absorbed by the surface - of hydroxyapatite crystals on the teeth, which are necessary for mineralization. - This renders the teeth more resistant to demineralization by changing the apatite - crystal solubility.[A181670,A181694] Sodium fluoride inhibits the demineralization - of teeth in a pH-related manner. When used in high doses, in formulations such - as the fluoride varnishes or gels, sodium fluoride forms a layer on the surface - of tooth enamel. When the pH of the mouth is reduced due to acid production by - bacteria such as S.mutans, fluoride is released, interfering with bacterial metabolism, - and then acts to remineralize the teeth.[A181652,A181694,L7688] - - - === - - - disease: Avitaminosis - - drug: Sodium fluoride - - ' -- completion: 'disease: Endocarditis, Bacterial - - drug: Cefapirin - - mechanism_links: Cephapirin - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - positively regulates - peptidoglycan-protein cross-linking; peptidoglycan-protein - cross-linking - positively regulates - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - has output - cell wall; cell wall - - occurs in - Staphylococcus aureus; Staphylococcus aureus - causes - Endocarditis, - Bacterial - - references: https://go.drugbank.com/drugs/DB01139; https://en.wikipedia.org/wiki/Infective_endocarditis#Cause' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal activity of cephapirin results from the inhibition of cell wall - synthesis via affinity for penicillin-binding proteins (PBPs). - - - === - - - disease: Endocarditis, Bacterial - - drug: Cefapirin - - ' -- completion: 'disease: Ovarian Neoplasms - - drug: Cisplatin - - mechanism_links: Cisplatin - negatively regulates - DNA synthesis involved in - DNA replication; Cisplatin - negatively regulates - DNA-templated transcription; - Cisplatin - disrupts - DNA; DNA synthesis involved in DNA replication - part of - - HP:0031377; DNA-templated transcription - part of - HP:0031377; DNA - participates - in - HP:0031377; HP:0031377 - positively correlated with - Ovarian Neoplasms - - references: https://go.drugbank.com/drugs/DB00515' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Alkylating agents work by three different mechanisms: 1) attachment of alkyl groups - to DNA bases, resulting in the DNA being fragmented by repair enzymes in their - attempts to replace the alkylated bases, preventing DNA synthesis and RNA transcription - from the affected DNA, 2) DNA damage via the formation of cross-links (bonds between - atoms in the DNA) which prevents DNA from being separated for synthesis or transcription, - and 3) the induction of mispairing of the nucleotides leading to mutations. - - - === - - - disease: Ovarian Neoplasms - - drug: Cisplatin - - ' -- completion: 'disease: Bipolar Disorder - - drug: Doxepin - - mechanism_links: Doxepin - decreases activity of - sodium-dependent serotonin - transporter (human); Doxepin - decreases activity of - sodium-dependent noradrenaline - transporter (human); sodium-dependent serotonin transporter (human) - participates - in - serotonin uptake; sodium-dependent noradrenaline transporter (human) - participates - in - norepinephrine uptake; norepinephrine uptake - decreases abundance of - Norepinephrine; - serotonin uptake - decreases abundance of - Serotonin; Serotonin - positively - correlated with - serotonin secretion, neurotransmission; Norepinephrine - positively - correlated with - norepinephrine secretion, neurotransmission; serotonin secretion, - neurotransmission - negatively regulates - Bipolar Disorder; norepinephrine secretion, - neurotransmission - negatively regulates - Bipolar Disorder - - references: https://go.drugbank.com/drugs/DB01142; https://en.wikipedia.org/wiki/Doxepin; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1628227/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Doxepin exact mechanism of action is not very clear. However, doxepin is known - to be a selective histamine H1 receptor blocker.[A177163] This effect on histamine - receptors indicates effectiveness in skin conditions.[T249] It is known that the - lack of dopamine transporters in the frontal cortex and the transmission of dopamine - in this region is largely inactivated by the effect of norepinephrine reuptake. - Hence, doxepin action on the frontal cortex is suggested to increase dopamine - neurotransmission in this area.[T249] - - - === - - - disease: Bipolar Disorder - - drug: Doxepin - - ' -- completion: 'disease: Chancroid - - drug: Ofloxacin - - mechanism_links: Ofloxacin - negatively regulates - InterPro:IPR013759; InterPro:IPR013759 - - positively regulates - DNA topological change; DNA topological change - in taxon - - NCBITaxon:730; NCBITaxon:730 - causes - Chancroid - - references: https://en.wikipedia.org/wiki/Ofloxacin#Mode_of_action; https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL2311224/; - https://go.drugbank.com/drugs/DB01165' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ofloxacin acts on DNA gyrase and toposiomerase IV, enzymes which, like human topoisomerase, - prevents the excessive supercoiling of DNA during replication or transcription. - By inhibiting their function, the drug thereby inhibits normal cell division. - - - === - - - disease: Chancroid - - drug: Ofloxacin - - ' -- completion: 'disease: Bronchiectasis - - drug: Acetylcysteine - - mechanism_links: Acetylcysteine - has metabolite - cysteine; cysteine - decreases - abundance of - mucus; cysteine - subclass of - mucolytic; mucolytic - negatively - correlated with - Bronchiectasis; mucus - positively correlated with - Bronchiectasis - - references: https://en.wikipedia.org/wiki/Acetylcysteine#Pharmacodynamics; https://pubchem.ncbi.nlm.nih.gov/compound/12035#section=Mechanism-of-Action; - https://en.wikipedia.org/wiki/Acetylcysteine#Lungs; https://en.wikipedia.org/wiki/Bronchiectasis#Airway_clearance' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nAcetylcysteine protects against acetaminophen overdose-induced hepatotoxicity\ - \ by maintaining or restoring hepatic concentrations of glutathione. It does this\ - \ by producing the glutathione precursor L-cysteine. Glutathione is required to\ - \ inactivate an intermediate metabolite (N-acetyl-p-benzoquinoneimine or NAPQI)\ - \ of acetaminophen that is thought to be hepatotoxic. In acetaminophen overdose\ - \ cases, excessive quantities of this metabolite are formed because the primary\ - \ metabolic (glucuronide and sulfate conjugation) pathways become saturated. Acetylcysteine\ - \ may act by reducing the metabolite to the parent compound and/or by providing\ - \ sulfhydryl for conjugation of the metabolite. Experimental evidence also suggests\ - \ that a sulfhydryl-containing compound such as acetylcysteine may also directly\ - \ inactivate the metabolite. The mechanisms of action for acetylcysteine\u2019\ - s well-known mucolytic effects are different. In particular, when inhaled, acetylcysteine\ - \ (and its metabolic byproduct cysteine) exerts its mucolytic action through its\ - \ free sulfhydryl group, which reduces the disulfide bonds in the mucus matrix\ - \ and lowers mucus viscosity. This action increases with increasing pH and is\ - \ most significant at pH 7 to 9. The mucolytic action of acetylcysteine is not\ - \ affected by the presence of DNA. Acetylcysteine is also an antioxidant and reduces\ - \ oxidative stress. Acetylcysteine serves as a prodrug to L-cysteine which is\ - \ a precursor to the biologic antioxidant, glutathione and hence administration\ - \ of acetylcysteine replenishes glutathione stores. L-cysteine also serves as\ - \ a precursor to cystine which in turn serves as a substrate for the cystine-glutamate\ - \ antiporter on astrocytes hence increasing glutamate release into the extracellular\ - \ space. This glutamate in turn acts on mGluR2/3 receptors, and at higher doses\ - \ of acetylcysteine, mGluR5. Glutathione also modulates the NMDA receptor by acting\ - \ at the redox site. These effects on glutamate and NMDA signaling appear to explain\ - \ some of the positive neuropsychotropic effects associated with NAC. Acetylcysteine\ - \ also possesses some anti-inflammatory effects possibly via inhibiting NF-\u03BA\ - B through redox activation of the nuclear factor kappa kinases thereby modulating\ - \ cytokine synthesis.\n\n===\n\ndisease: Bronchiectasis\ndrug: Acetylcysteine\n" -- completion: 'disease: Intraabdominal Infections - - drug: Ticarcillin - - mechanism_links: Ticarcillin - negatively regulates - InterPro:IPR001460; InterPro:IPR001460 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Escherichia coli; Escherichia - coli - causes - Intraabdominal Infections - - references: https://go.drugbank.com/drugs/DB01607' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ticarcillin''s principal mechanism of action revolves around its capacity to prevent - the cross-linking of peptidoglycan during bacterial cell wall synthesis. Consequently, - when the offending bacteria attempt to undergo cell division, cell death occurs. - - - === - - - disease: Intraabdominal Infections - - drug: Ticarcillin - - ' -- completion: 'disease: Cough - - drug: Benzocaine - - mechanism_links: Benzocaine - decreases activity of - sodium channel protein type - 10 subunit alpha (human); sodium channel protein type 10 subunit alpha (human) - - participates in - voltage-gated sodium channel activity; voltage-gated sodium - channel activity - increases transport of - Sodium; Sodium - positively correlated - with - membrane depolarization; membrane depolarization - positively regulates - - neuronal action potential; neuronal action potential - occurs in - pain receptor - cell; pain receptor cell - participates in - sensory perception of pain; sensory - perception of pain - occurs in - Cough - - references: https://go.drugbank.com/drugs/DB01086; https://en.wikipedia.org/wiki/Benzocaine' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Benzocaine binds to sodium channels and reversibly stabilizes the neuronal membrane - which decreases its permeability to sodium ions. Depolarization of the neuronal - membrane is inhibited thereby blocking the initiation and conduction of nerve - impulses. - - - === - - - disease: Cough - - drug: Benzocaine - - ' -- completion: 'disease: Arthritis, Juvenile - - drug: Etodolac - - mechanism_links: Etodolac - decreases activity of - prostaglandin G/H synthase - 2 (human); Etodolac - decreases activity of - prostaglandin G/H synthase 1 (human); - prostaglandin G/H synthase 2 (human) - increases abundance of - Prostaglandins; - prostaglandin G/H synthase 1 (human) - increases abundance of - Prostaglandins; - Prostaglandins - participates in - inflammatory response; inflammatory response - - causes - Pain; Pain - occurs in - Arthritis, Juvenile - - references: https://go.drugbank.com/drugs/DB00749; https://pubmed.ncbi.nlm.nih.gov/1714278/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nSimilar to other NSAIDs, the anti-inflammatory effects of etodolac\ - \ result from inhibition of the enzyme cycooxygenase (COX). This decreases the\ - \ synthesis of peripheral prostaglandins involved in mediating inflammation. Etodolac\ - \ binds to the upper portion of the COX enzyme active site and prevents its substrate,\ - \ arachidonic acid, from entering the active site. Etodolac was previously thought\ - \ to be a non-selective COX inhibitor, but it is now known to be 5 \u2013 50 times\ - \ more selective for COX-2 than COX-1. Antipyresis may occur by central action\ - \ on the hypothalamus, resulting in peripheral dilation, increased cutaneous blood\ - \ flow, and subsequent heat loss.\n\n===\n\ndisease: Arthritis, Juvenile\ndrug:\ - \ Etodolac\n" -- completion: 'disease: Endometritis - - drug: Imipenem - - mechanism_links: Imipenem - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - in taxon - Bacteria; Bacteria - causes - Endometritis - - references: https://go.drugbank.com/drugs/DB01598#mechanismofaction; https://en.wikipedia.org/wiki/Imipenem#Mechanism_of_action; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL148/; https://pubchem.ncbi.nlm.nih.gov/compound/104838' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Imipenem acts as an antimicrobial through the inhibition of cell wall synthesis - of various gram-positive and gram-negative bacteria.[L7526,L7568] This inhibition - of cell wall synthesis in gram-negative bateria is attained by binding to penicillin-binding - proteins (PBPs). In E. coli and selected strains of P. aeruginosa, imipenem has - shown to have the highest affinity to PBP-2, PBP-1a, and PBP-1b.[A15388] This - inhibition of PBPs prevents the bacterial cell from adding to the peptidoglycan - polymer which forms the bacterial cell wall eventually leading to cell death.[T116] - - - === - - - disease: Endometritis - - drug: Imipenem - - ' -- completion: 'disease: Appendicitis - - drug: Piperacillin - - mechanism_links: Piperacillin - negatively regulates - Pfam:PF00905; Pfam:PF00905 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively correlated with - peptidoglycan-based cell wall biogenesis; - peptidoglycan-based cell wall biogenesis - in taxon - Escherichia coli; Escherichia - coli - causes - Appendicitis - - references: https://go.drugbank.com/drugs/DB00319; https://pubmed.ncbi.nlm.nih.gov/23231389/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, Piperacillin inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that Piperacillin interferes with an autolysin - inhibitor. - - - === - - - disease: Appendicitis - - drug: Piperacillin - - ' -- completion: 'disease: Scrub Typhus - - drug: Fusidic acid - - mechanism_links: Fusidic Acid - decreases activity of - PR:B3CTE7; PR:B3CTE7 - - positively regulates - translation; translation - occurs in - NCBITaxon:784; NCBITaxon:784 - - causes - Scrub Typhus - - references: https://go.drugbank.com/drugs/DB02703#mechanism-of-action; https://en.wikipedia.org/wiki/Fusidic_acid; - https://www.uniprot.org/uniprot/B3CTE7#function; https://en.wikipedia.org/wiki/Scrub_typhus' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fusidic acid works by interfering with bacterial protein synthesis, specifically - by preventing the translocation of the elongation factor G (EF-G) from the ribosome. - It also can inhibit chloramphenicol acetyltransferase enzymes. - - - === - - - disease: Scrub Typhus - - drug: Fusidic acid - - ' -- completion: 'disease: MESH:D000080223 - - drug: Astemizole - - mechanism_links: Astemizole - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - cellular response to histamine - positively correlated with - positive regulation - of vascular permeability; cellular response to histamine - positively correlated - with - HP:0000969; HP:0000969 - manifestation of - MESH:D000080223; positive regulation - of vascular permeability - manifestation of - MESH:D000080223; inflammatory response - - causes - MESH:D000080223 - - references: https://go.drugbank.com/drugs/DB00637' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Astemizole competes with histamine for binding at H<sub>1</sub>-receptor - sites in the GI tract, uterus, large blood vessels, and bronchial muscle. This - reversible binding of astemizole to H<sub>1</sub>-receptors suppresses - the formation of edema, flare, and pruritus resulting from histaminic activity. - As the drug does not readily cross the blood-brain barrier and preferentially - binds at H1 receptors in the peripehery rather than within the brain, CNS depression - is minimal. Astemizole may also act on H<sub>3</sub>-receptors, producing - adverse effects. - - - === - - - disease: MESH:D000080223 - - drug: Astemizole - - ' -- completion: 'disease: Klinefelter Syndrome - - drug: Fluoxymesterone - - mechanism_links: Fluoxymesterone - increases activity of - androgen receptor (human); - androgen receptor (human) - positively regulates - androgen receptor signaling - pathway; androgen receptor signaling pathway - positively correlated with - development - of secondary male sexual characteristics; development of secondary male sexual - characteristics - negatively correlated with - Klinefelter Syndrome - - references: https://go.drugbank.com/drugs/DB01185; https://en.wikipedia.org/wiki/Fluoxymesterone; - https://en.wikipedia.org/wiki/Androgen' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Fluoxymesterone is a synthetic androgenic anabolic steroid and is approximately - 5 times as potent as natural methyltestosterone. Like testosterone and other androgenic - hormones, fluoxymesterone binds to the androgen receptor. It produces retention - of nitrogen, sodium, potassium, and phosphorus; increases protein anabolism; decreases - amino acid catabolism and decreased urinary excretion of calcium. The antitumour - activity of fluoxymesterone appears related to reduction or competitive inhibition - of prolactin receptors or estrogen receptors or production. - - - === - - - disease: Klinefelter Syndrome - - drug: Fluoxymesterone - - ' -- completion: 'disease: Klebsiella Infections - - drug: Moxifloxacin - - mechanism_links: MESH:D000077266 - decreases activity of - PR:A6TBT6; MESH:D000077266 - - decreases activity of - PR:A6TE12; PR:A6TBT6 - positively regulates - DNA replication; - PR:A6TE12 - positively regulates - DNA replication; DNA replication - occurs in - - NCBITaxon:570; NCBITaxon:570 - causes - Klebsiella Infections - - references: https://go.drugbank.com/drugs/DB00218#mechanism-of-action; https://www.uniprot.org/uniprot/A6TBT6#function; - https://www.uniprot.org/uniprot/A6TE12#function; https://en.wikipedia.org/wiki/Klebsiella#In_humans' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The bactericidal action of moxifloxacin results from inhibition of the enzymes - topoisomerase II (DNA gyrase) and topoisomerase IV. DNA gyrase is an essential - enzyme that is involved in the replication, transcription and repair of bacterial - DNA. Topoisomerase IV is an enzyme known to play a key role in the partitioning - of the chromosomal DNA during bacterial cell division. - - - === - - - disease: Klebsiella Infections - - drug: Moxifloxacin - - ' -- completion: 'disease: Tuberculosis, Pulmonary - - drug: Ethambutol - - mechanism_links: Ethambutol - decreases activity of - PR:P9WNL5; Ethambutol - - decreases activity of - PR:P9WNL7; Ethambutol - decreases activity of - probable - arabinosyltransferase A (Mycobacterium tuberculosis H37Rv); PR:P9WNL5 - positively - regulates - Actinobacterium-type cell wall biogenesis; PR:P9WNL7 - positively - regulates - Actinobacterium-type cell wall biogenesis; probable arabinosyltransferase - A (Mycobacterium tuberculosis H37Rv) - positively regulates - Actinobacterium-type - cell wall biogenesis; Actinobacterium-type cell wall biogenesis - positively correlated - with - cell division; cell division - in taxon - Mycobacterium tuberculosis; Mycobacterium - tuberculosis - causes - Tuberculosis, Pulmonary - - references: https://go.drugbank.com/drugs/DB00330' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Ethambutol inhibits arabinosyl transferases which is involved in cell wall biosynthesis. - By inhibiting this enzyme, the bacterial cell wall complex production is inhibited. - This leads to an increase in cell wall permeability. - - - === - - - disease: Tuberculosis, Pulmonary - - drug: Ethambutol - - ' -- completion: 'disease: Tendinopathy - - drug: Triamcinolone - - mechanism_links: Triamcinolone Acetonide - increases activity of - glucocorticoid - receptor (human); glucocorticoid receptor (human) - increases activity of - annexin - A1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 1 (human); glucocorticoid receptor (human) - decreases activity of - - prostaglandin G/H synthase 2 (human); annexin A1 (human) - decreases activity - of - cytosolic phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - - positively regulates - prostaglandin biosynthetic process; prostaglandin G/H - synthase 2 (human) - positively regulates - prostaglandin biosynthetic process; - cytosolic phospholipase A2 (human) - positively regulates - leukotriene biosynthetic - process; cytosolic phospholipase A2 (human) - positively regulates - prostaglandin - biosynthetic process; leukotriene biosynthetic process - positively correlated - with - inflammatory response; prostaglandin biosynthetic process - positively - correlated with - inflammatory response; inflammatory response - has phenotype - - HP:0012531; HP:0012531 - located in - tendon; tendon - location of - Tendinopathy - - references: https://go.drugbank.com/drugs/DB00620#mechanism-of-action; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Tendinopathy' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Corticosteroids like triamcinolone inhibit phospholipase A2 on cell membranes, - preventing the breakdown of lysosomal membranes of leukocytes, which in turn prevent - the formation of arachidonic acid, which decrease expression of cyclooxygenase - and lipoxygenase, inhibiting synthesis of prostaglandins and leukotrienes.[A184463] - Anti-inflammatory activity occurs via reversal of vascular dilation and reducing - permeability, which prevents macrophage and leukocyte migration.[A184463] Triamcinolone - also inhibits nuclear factor kappa-B, which decreases the production of pro-inflammatory - signals such as interleukin-6, interleukin-8, and monocyte chemoattractant protein-1.[A184463] - - - === - - - disease: Tendinopathy - - drug: Triamcinolone - - ' -- completion: 'disease: Hot Flashes - - drug: Paroxetine - - mechanism_links: Paroxetine - decreases activity of - sodium-dependent serotonin - transporter (human); sodium-dependent serotonin transporter (human) - positively - regulates - serotonin uptake; serotonin uptake - decreases abundance of - Serotonin; - Serotonin - positively correlated with - serotonin secretion, neurotransmission; - serotonin secretion, neurotransmission - treats - Hot Flashes - - references: https://go.drugbank.com/drugs/DB00715#BE0000749; https://drugs.ncats.io/drug/41VRH5220H; - https://en.wikipedia.org/wiki/Hot_flash#Mechanism' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nParoxetine enhances serotonergic activity via the inhibition presynaptic\ - \ reuptake of serotonin by the serotonin (SERT) receptor.[A5492,A181772] This\ - \ inhibition raises the level of serotonin in the synaptic cleft, relieving various\ - \ symptoms. This drug has been demonstrated to be a stronger inhibitor of serotonin\ - \ reuptake than other members of the same drug class, including [Citalopram],\ - \ [Fluoxetine], and [Fluvoxamine].[A31914] The mechanism of action of paroxetine\ - \ in relieving the vasomotor symptoms of menopause is unknown, according to the\ - \ Brisdelle prescribing information[L7703], but may occur due to its effects on\ - \ thermoregulation.[A181973] Paroxetine shows a clinically insignificant affinity\ - \ for adrenergic alpha-1 and alpha-2 receptors and \u03B2-adrenergic receptors,\ - \ dopamine D1 and D2 receptors, histamine H1 receptors and serotonin 5-HT1A, 5-HT2A\ - \ and 5-HT2C receptors.[A31914] This drug shows some affinity for muscarinic cholinergic\ - \ receptors and 5-H2B receptors.[A181829,A181847] The delayed onset of paroxetine\ - \ therapeutic effects may be explained by the initial paroxetine actions on the\ - \ 5-HT neurons. In rats, paroxetine activates 5-HT1A receptors when it is first\ - \ administered, inhibiting the stimulation of the 5-HT neurons and subsequent\ - \ release of serotonin at the synaptic cleft.[A31914]\n\n===\n\ndisease: Hot Flashes\n\ - drug: Paroxetine\n" -- completion: 'disease: Lymphoma, Non-Hodgkin - - drug: Thiotepa - - mechanism_links: Thiotepa - disrupts - DNA; DNA - participates in - DNA replication; - DNA replication - precedes - lymphocyte proliferation; lymphocyte proliferation - - positively correlated with - Lymphoma, Non-Hodgkin - - references: https://go.drugbank.com/drugs/DB04572; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL671/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The alkyl group is attached to the guanine base of DNA, at the number 7 nitrogen - atom of the imidazole ring. They stop tumor growth by crosslinking guanine nucleobases - in DNA double-helix strands, directly attacking DNA. This makes the strands unable - to uncoil and separate. As this is necessary in DNA replication, the cells can - no longer divide. These drugs act nonspecifically. - - - === - - - disease: Lymphoma, Non-Hodgkin - - drug: Thiotepa - - ' -- completion: 'disease: Nephrotic Syndrome - - drug: Prednisone - - mechanism_links: Prednisone - has metabolite - Prednisolone; Prednisolone - increases - activity of - glucocorticoid receptor (human); glucocorticoid receptor (human) - - increases activity of - annexin A1 (human); glucocorticoid receptor (human) - - decreases activity of - prostaglandin G/H synthase 1 (human); glucocorticoid - receptor (human) - decreases activity of - prostaglandin G/H synthase 2 (human); - annexin A1 (human) - decreases activity of - cytosolic phospholipase A2 (human); - prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin biosynthetic - process; prostaglandin G/H synthase 2 (human) - positively regulates - prostaglandin - biosynthetic process; cytosolic phospholipase A2 (human) - positively regulates - - leukotriene biosynthetic process; cytosolic phospholipase A2 (human) - positively - regulates - prostaglandin biosynthetic process; leukotriene biosynthetic process - - positively correlated with - inflammatory response; prostaglandin biosynthetic - process - positively correlated with - inflammatory response; inflammatory response - - positively correlated with - Nephrotic Syndrome - - references: https://go.drugbank.com/drugs/DB00635#mechanism-of-action; https://en.wikipedia.org/wiki/Prednisone; - https://www.uniprot.org/uniprot/P04150#function; https://www.uniprot.org/uniprot/P04083#function; - https://www.uniprot.org/uniprot/P47712#function; https://www.uniprot.org/uniprot/P23219#function; - https://www.uniprot.org/uniprot/P35354#function; https://en.wikipedia.org/wiki/Nephrotic_syndrome' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Prednisone is first metabolized in the liver to its active form, prednisolone, - a glucocorticoid agonist corticosteroid.[L10502] Lower doses of corticosteroids - provide an anti-inflammatory effect, while higher doses are immunosuppressive.[A187463] - High doses of glucocorticoids for an extended period bind to the mineralocorticoid - receptor, raising sodium levels and decreasing potassium levels.[A187463] - - - === - - - disease: Nephrotic Syndrome - - drug: Prednisone - - ' -- completion: 'disease: Arthralgia - - drug: Acetaminophen - - mechanism_links: Acetaminophen - decreases activity of - prostaglandin G/H synthase - 1 (human); Acetaminophen - decreases activity of - prostaglandin G/H synthase - 2 (human); Acetaminophen - decreases activity of - prostaglandin E synthase 3 - (human); prostaglandin G/H synthase 1 (human) - positively regulates - prostaglandin - biosynthetic process; prostaglandin G/H synthase 2 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin E synthase 3 (human) - positively - regulates - prostaglandin biosynthetic process; prostaglandin biosynthetic process - - increases abundance of - Prostaglandins; Prostaglandins - positively correlated - with - Arthralgia - - references: https://go.drugbank.com/drugs/DB00316#mechanism-of-action; https://www.uniprot.org/uniprot/P23219#function; - https://www.uniprot.org/uniprot/P35354#function; https://www.uniprot.org/uniprot/Q15185#function; - https://en.wikipedia.org/wiki/Arthralgia' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - According to its FDA labeling, acetaminophen''s exact mechanism of action has - not been fully established[Label] - despite this, it is often categorized alongside - NSAIDs (nonsteroidal anti-inflammatory drugs) due to its ability to inhibit the - cyclooxygenase (COX) pathways.[T518] It is thought to exert central actions which - ultimately lead to the alleviation of pain symptoms.[T518] One theory is that - acetaminophen increases the pain threshold by inhibiting two isoforms of cyclooxygenase, - COX-1 and COX-2, which are involved in prostaglandin (PG) synthesis. Prostaglandins - are responsible for eliciting pain sensations.[A176366] Acetaminophen does not - inhibit cyclooxygenase in peripheral tissues and, therefore, has no peripheral - anti-inflammatory effects. Though acetylsalicylic acid (aspirin) is an irreversible - inhibitor of COX and directly blocks the active site of this enzyme, studies have - shown that acetaminophen (paracetamol) blocks COX indirectly.[F4133] Studies also - suggest that acetaminophen selectively blocks a variant type of the COX enzyme - that is unique from the known variants COX-1 and COX-2.[A468] This enzyme has - been referred to as _COX-3_. The antipyretic actions of acetaminophen are likely - attributed to direct action on heat-regulating centers in the brain, resulting - in peripheral vasodilation, sweating, and loss of body heat.[F4133] The exact - mechanism of action of this drug is not fully understood at this time, but future - research may contribute to deeper knowledge.[F4133] - - - === - - - disease: Arthralgia - - drug: Acetaminophen - - ' -- completion: 'disease: Acne Vulgaris - - drug: Clotrimazole - - mechanism_links: Adapalene - positively regulates - Receptors, Retinoic Acid; - Receptors, Retinoic Acid - negatively regulates - keratinization; keratinization - - increases abundance of - HP:0025249; HP:0025249 - positively correlated with - - Acne Vulgaris - - references: https://go.drugbank.com/drugs/DB00210#mechanism-of-action; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374937/; - https://en.wikipedia.org/wiki/Adapalene#Pharmacodynamics; https://pubmed.ncbi.nlm.nih.gov/19929446/' - prompt: "From the text below, extract the following entities in the following format:\n\ - \ndisease: \ndrug: \nmechanism_links: \n\ - \n\nText:\nClotrimazole acts primarily by damaging the permeability barrier in\ - \ the cell membrane of fungi. Clotrimazole causes inhibition of ergosterol biosynthesis,\ - \ an essential constituent of fungal cell membranes. If ergosterol synthesis is\ - \ either completely or partially inhibited, the cell is no longer able to construct\ - \ an intact and functional cell membrane [F3088],[F3100]. Because ergosterol directly\ - \ promotes the growth of fungal cells in a hormone\u2010like fashion, rapid onset\ - \ of the above events leads to dose-dependent inhibition of fungal growth [A174094].\ - \ Though decreased ergosterol, due to the inhibition of lanosterol 14-demethylase\ - \ (also known as _CYP51_) [A174094] is accepted to be primarily responsible for\ - \ the antimycotic properties of clotrimazole, this drug also shows other pharmacological\ - \ effects. These include the inhibition of sarcoplasmic reticulum Ca2+\u2010ATPase,\ - \ depletion of intracellular calcium, and blocking of calcium\u2010dependent\ - \ potassium channels and voltage\u2010dependent calcium channels [A174094]. The\ - \ action of clotrimazole on these targets accounts for other effects of this drug\ - \ that are separate from its antimycotic activities [A174094].\n\n===\n\ndisease:\ - \ Acne Vulgaris\ndrug: Clotrimazole\n" -- completion: 'disease: Irritable Bowel Syndrome - - drug: Dicyclomine - - mechanism_links: Dicyclomine - decreases activity of - muscarinic acetylcholine - receptor M3 (human); muscarinic acetylcholine receptor M3 (human) - participates - in - response to acetylcholine; response to acetylcholine - positively regulates - - smooth muscle contraction; smooth muscle contraction - positively regulates - - intestinal motility; smooth muscle contraction - positively regulates - defecation; - intestinal motility - occurs in - Irritable Bowel Syndrome; defecation - occurs - in - Irritable Bowel Syndrome; Dicyclomine - negatively regulates - response to - histamine; response to histamine - positively correlated with - Irritable Bowel - Syndrome - - references: https://go.drugbank.com/drugs/DB00804; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1123/; - https://drugs.ncats.io/drug/4KV4X8IF6V' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Dicyclomine achieves its action partially through direct antimuscarinic activity - of the M1 and M2 receptors, and partially through antagonism of bradykinin and - histamine.[A6556,A182555,L7967] Dicyclomine non-competitively inhibits the action - of bradykinin and histamine, resulting in direct action on the smooth muscle, - and decreased strength of contractions seen in spasms of the ileum.[A182555] - - - === - - - disease: Irritable Bowel Syndrome - - drug: Dicyclomine - - ' -- completion: 'disease: Alcohol Withdrawal Delirium - - drug: Diazepam - - mechanism_links: Diazepam - positively regulates - GABA receptor activity; GABA - receptor activity - positively regulates - GABA-gated chloride ion channel activity; - GABA receptor activity - positively correlated with - gamma-aminobutyric acid - secretion, neurotransmission; GABA-gated chloride ion channel activity - negatively - regulates - neuronal action potential; neuronal action potential - positively - regulates - glutamate secretion, neurotransmission; gamma-aminobutyric acid secretion, - neurotransmission - negatively correlated with - Alcohol Withdrawal Delirium; - glutamate secretion, neurotransmission - positively correlated with - Seizures; - Seizures - manifestation of - Alcohol Withdrawal Delirium - - references: https://go.drugbank.com/drugs/DB00829#BE0004797; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1312739/' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Diazepam is a benzodiazepine tranquilliser with anticonvulsant, sedative, muscle - relaxant and amnesic properties [F3157, F3160, L5188]. Benzodiazepines, such as - diazepam, bind to receptors in various regions of the brain and spinal cord. This - binding increases the inhibitory effects of gamma-aminobutyric acid (GABA) [F3157, - F3160, L5188]. GABAs functions include CNS involvement in sleep induction. Also - involved in the control of hypnosis, memory, anxiety, epilepsy and neuronal excitability - [F3157, F3160, L5188]. - - - === - - - disease: Alcohol Withdrawal Delirium - - drug: Diazepam - - ' -- completion: 'disease: Nausea - - drug: Triflupromazine - - mechanism_links: Triflupromazine - decreases activity of - D(2) dopamine receptor - (human); D(2) dopamine receptor (human) - located in - area postrema; area postrema - - negatively regulates - vagus nerve; vagus nerve - located in - upper digestive - tract; upper digestive tract - prevents - Nausea - - references: https://go.drugbank.com/drugs/DB00508#mechanismofaction' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Triflupromazine binds to the dopamine D1 and dopamine D2 receptors and inhibits - their activity. The mechanism of the anti-emetic effect is due predominantly to - blockage of the dopamine D2 neurotransmitter receptors in the chemoreceptor trigger - zone (CTZ) and vomiting centre. Triflupromazine blocks the neurotransmitter dopamine - and the vagus nerve in the gastrointestinal tract. Triflupromazine also binds - the muscarinic acetylcholine receptors (M1 and M2) and the tryptamine D receptors - (5HT<sub>2B</sub>). - - - === - - - disease: Nausea - - drug: Triflupromazine - - ' -- completion: 'disease: Psoriasis - - drug: Cortisone acetate - - mechanism_links: Cortisone - increases activity of - glucocorticoid receptor (human); - glucocorticoid receptor (human) - increases activity of - annexin A1 (human); - glucocorticoid receptor (human) - decreases activity of - prostaglandin G/H synthase - 1 (human); glucocorticoid receptor (human) - decreases activity of - prostaglandin - G/H synthase 2 (human); annexin A1 (human) - decreases activity of - cytosolic - phospholipase A2 (human); prostaglandin G/H synthase 1 (human) - positively regulates - - prostaglandin biosynthetic process; prostaglandin G/H synthase 2 (human) - positively - regulates - prostaglandin biosynthetic process; cytosolic phospholipase A2 (human) - - positively regulates - leukotriene biosynthetic process; cytosolic phospholipase - A2 (human) - positively regulates - prostaglandin biosynthetic process; leukotriene - biosynthetic process - positively correlated with - inflammatory response; prostaglandin - biosynthetic process - positively correlated with - inflammatory response; inflammatory - response - positively correlated with - HP:0011123; HP:0011123 - positively correlated - with - Psoriasis - - references: https://go.drugbank.com/drugs/DB01380#mechanism-of-action; https://www.uniprot.org/uniprot/P04150#function; - https://www.uniprot.org/uniprot/P04083#function; https://www.uniprot.org/uniprot/P47712#function; - https://www.uniprot.org/uniprot/P23219#function; https://www.uniprot.org/uniprot/P35354#function; - https://en.wikipedia.org/wiki/Psoriasis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Cortisone acetate binds to the cytosolic glucocorticoid receptor. After binding - the receptor the newly formed receptor-ligand complex translocates itself into - the cell nucleus, where it binds to many glucocorticoid response elements (GRE) - in the promoter region of the target genes. The DNA bound receptor then interacts - with basic transcription factors, causing the increase in expression of specific - target genes. The anti-inflammatory actions of corticosteroids are thought to - involve lipocortins, phospholipase A2 inhibitory proteins which, through inhibition - arachidonic acid, control the biosynthesis of prostaglandins and leukotrienes. - Specifically glucocorticoids induce lipocortin-1 (annexin-1) synthesis, which - then binds to cell membranes preventing the phospholipase A2 from coming into - contact with its substrate arachidonic acid. This leads to diminished eicosanoid - production. The cyclooxygenase (both COX-1 and COX-2) expression is also suppressed, - potentiating the effect. In other words, the two main products in inflammation - Prostaglandins and Leukotrienes are inhibited by the action of Glucocorticoids. - Glucocorticoids also stimulate the lipocortin-1 escaping to the extracellular - space, where it binds to the leukocyte membrane receptors and inhibits various - inflammatory events: epithelial adhesion, emigration, chemotaxis, phagocytosis, - respiratory burst and the release of various inflammatory mediators (lysosomal - enzymes, cytokines, tissue plasminogen activator, chemokines etc.) from neutrophils, - macrophages and mastocytes. Additionally the immune system is suppressed by corticosteroids - due to a decrease in the function of the lymphatic system, a reduction in immunoglobulin - and complement concentrations, the precipitation of lymphocytopenia, and interference - with antigen-antibody binding. - - - === - - - disease: Psoriasis - - drug: Cortisone acetate - - ' -- completion: 'disease: Mycosis Fungoides - - drug: Mechlorethamine - - mechanism_links: Mechlorethamine - disrupts - DNA; DNA - participates in - DNA - replication; DNA replication - occurs in - HP:0031377; HP:0031377 - occurs in - - Mycosis Fungoides - - references: https://go.drugbank.com/drugs/DB00888' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Alkylating agents work by three different mechanisms: 1) attachment of alkyl groups - to DNA bases, resulting in the DNA being fragmented by repair enzymes in their - attempts to replace the alkylated bases, preventing DNA synthesis and RNA transcription - from the affected DNA, 2) DNA damage via the formation of cross-links (bonds between - atoms in the DNA) which prevents DNA from being separated for synthesis or transcription, - and 3) the induction of mispairing of the nucleotides leading to mutations. Mechlorethamine - is cell cycle phase-nonspecific. - - - === - - - disease: Mycosis Fungoides - - drug: Mechlorethamine - - ' -- completion: 'disease: Chorioretinitis - - drug: Sulfadiazine - - mechanism_links: Sulfadiazine - negatively regulates - InterPro:IPR006390; InterPro:IPR006390 - - positively regulates - folic acid biosynthetic process; folic acid biosynthetic - process - in taxon - NCBITaxon:5811; NCBITaxon:5811 - causes - Chorioretinitis - - references: https://go.drugbank.com/drugs/DB00359; https://en.wikipedia.org/wiki/Sulfadiazine#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Sulfadiazine is a competitive inhibitor of the bacterial enzyme dihydropteroate - synthetase. This enzyme is needed for the proper processing of para-aminobenzoic - acid (PABA) which is essential for folic acid synthesis. The inhibited reaction - is necessary in these organisms for the synthesis of folic acid. - - - === - - - disease: Chorioretinitis - - drug: Sulfadiazine - - ' -- completion: 'disease: Ascites - - drug: Spironolactone - - mechanism_links: Spironolactone - negatively regulates - mineralocorticoid receptor - (human); mineralocorticoid receptor (human) - positively correlated with - Aldosterone; - Aldosterone - contributes to - renal sodium ion absorption; renal sodium ion absorption - - positively correlated with - renal water retention; renal water retention - - contributes to - Ascites - - references: https://go.drugbank.com/drugs/DB00421; https://en.wikipedia.org/wiki/Ascites#:~:text=Ascites%20is%20the%20abnormal%20buildup,discomfort%2C%20and%20shortness%20of%20breath' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Spironolactone competitively inhibits aldosterone dependant sodium potassium exchange - channels in the distal convoluted tubule.[Label] This action leads to increased - sodium and water excretion, but more potassium retention.[Label] The increased - excretion of water leads to diuretic and also antihypertensive effects.[Label] - - - === - - - disease: Ascites - - drug: Spironolactone - - ' -- completion: 'disease: Intraabdominal Infections - - drug: Imipenem - - mechanism_links: Imipenem - decreases activity of - InterPro:IPR005311; InterPro:IPR005311 - - positively regulates - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - positively correlated with - cell division; cell division - - in taxon - Bacteria; Bacteria - causes - Intraabdominal Infections - - references: https://go.drugbank.com/drugs/DB01598#mechanismofaction; https://en.wikipedia.org/wiki/Imipenem#Mechanism_of_action; - https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL148/; https://pubchem.ncbi.nlm.nih.gov/compound/104838' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Imipenem acts as an antimicrobial through the inhibition of cell wall synthesis - of various gram-positive and gram-negative bacteria.[L7526,L7568] This inhibition - of cell wall synthesis in gram-negative bateria is attained by binding to penicillin-binding - proteins (PBPs). In E. coli and selected strains of P. aeruginosa, imipenem has - shown to have the highest affinity to PBP-2, PBP-1a, and PBP-1b.[A15388] This - inhibition of PBPs prevents the bacterial cell from adding to the peptidoglycan - polymer which forms the bacterial cell wall eventually leading to cell death.[T116] - - - === - - - disease: Intraabdominal Infections - - drug: Imipenem - - ' -- completion: 'disease: Trachoma - - drug: Meclocycline - - mechanism_links: meclocycline - decreases activity of - InterPro:IPR000235; InterPro:IPR000235 - - positively regulates - tRNA aminoacylation; tRNA aminoacylation - participates - in - translation; translation - in taxon - Chlamydia trachomatis; Chlamydia trachomatis - - causes - Trachoma - - references: https://go.drugbank.com/drugs/DB13092' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - As a tetracycline, meclocycline likely works by reversably associating with the - 30s subint of the bacterial ribosome [A19429]. A likely binding site for tetracyclines - has been identified on protein S7 of this subunit. This association blocks the - association of aminoacyl-tRNA with the ribosome, inhibiting protein synthesis. - Ultimately this inhibits bacterial growth due to a lack of proteins necessary - for reproduction. - - - === - - - disease: Trachoma - - drug: Meclocycline - - ' -- completion: 'disease: Dacryocystitis - - drug: Tobramycin - - mechanism_links: Tobramycin - negatively regulates - RNA, Ribosomal, 16S; Tobramycin - - negatively regulates - RNA, Ribosomal, 23S; RNA, Ribosomal, 16S - located in - - ribosome; RNA, Ribosomal, 23S - located in - ribosome; ribosome - positively - regulates - translation; translation - occurs in - Bacteria; Bacteria - causes - - Dacryocystitis - - references: https://go.drugbank.com/drugs/DB00684#mechanism-of-action; https://en.wikipedia.org/wiki/16S_ribosomal_RNA; - https://en.wikipedia.org/wiki/23S_ribosomal_RNA; https://en.wikipedia.org/wiki/Dacryocystitis' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tobramycin binds irreversibly to one of two aminoglycoside binding sites on the - 30 S ribosomal subunit, inhibiting bacterial protein synthesis. Tobramycin may - also destabilize bacterial memebrane by binding to 16 S 16 S r-RNA. An active - transport mechanism for aminoglycoside uptake is necessary in the bacteria in - order to attain a significant intracellular concentration of tobramycin. - - - === - - - disease: Dacryocystitis - - drug: Tobramycin - - ' -- completion: 'disease: Rhinitis, Vasomotor - - drug: Cyclizine - - mechanism_links: Cyclizine - decreases activity of - histamine H1 receptor (human); - histamine H1 receptor (human) - positively regulates - histamine receptor activity; - histamine receptor activity - participates in - cellular response to histamine; - cellular response to histamine - positively correlated with - inflammatory response; - inflammatory response - causes - Rhinitis, Vasomotor - - references: https://go.drugbank.com/drugs/DB01176; https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL648/; - https://en.wikipedia.org/wiki/Cyclizine' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Vomiting (emesis) is essentially a protective mechanism for removing irritant - or otherwise harmful substances from the upper GI tract. Emesis or vomiting is - controlled by the vomiting centre in the medulla region of the brain, an important - part of which is the chemotrigger zone (CTZ). The vomiting centre possesses neurons - which are rich in muscarinic cholinergic and histamine containing synapses. These - types of neurons are especially involved in transmission from the vestibular apparatus - to the vomiting centre. Motion sickness principally involves overstimulation of - these pathways due to various sensory stimuli. Hence the action of cyclizine which - acts to block the histamine receptors in the vomiting centre and thus reduce activity - along these pathways. Furthermore since cyclizine possesses anti-cholinergic properties - as well, the muscarinic receptors are similarly blocked. - - - === - - - disease: Rhinitis, Vasomotor - - drug: Cyclizine - - ' -- completion: 'disease: Syphilis, tertiary - - drug: Benzylpenicillin - - mechanism_links: Penicillin G - decreases activity of - InterPro:IPR001460; InterPro:IPR001460 - - participates in - peptidoglycan biosynthetic process; peptidoglycan biosynthetic - process - positively regulates - peptidoglycan-based cell wall biogenesis; peptidoglycan-based - cell wall biogenesis - occurs in - NCBITaxon:160; NCBITaxon:160 - causes - Syphilis, - tertiary - - references: https://go.drugbank.com/drugs/DB01053#mechanism-of-action; https://en.wikipedia.org/wiki/Syphilis#Tertiary' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - By binding to specific penicillin-binding proteins (PBPs) located inside the bacterial - cell wall, penicillin G inhibits the third and last stage of bacterial cell wall - synthesis. Cell lysis is then mediated by bacterial cell wall autolytic enzymes - such as autolysins; it is possible that penicillin G interferes with an autolysin - inhibitor. - - - === - - - disease: Syphilis, tertiary - - drug: Benzylpenicillin - - ' -- completion: 'disease: Rhinoscleroma - - drug: Amikacin - - mechanism_links: Amikacin - decreases activity of - PR:B5XN85; Amikacin - negatively - regulates - RNA, Ribosomal, 16S; PR:B5XN85 - part of - small ribosomal subunit; - RNA, Ribosomal, 16S - located in - small ribosomal subunit; small ribosomal subunit - - participates in - translation; translation - occurs in - NCBITaxon:39831; NCBITaxon:39831 - - causes - Rhinoscleroma - - references: https://go.drugbank.com/drugs/DB00479#mechanism-of-action; https://drugs.ncats.io/drug/84319SGC3C; - https://en.wikipedia.org/wiki/Amikacin#Mechanism_of_action; https://www.uniprot.org/uniprot/B5XN85#function; - https://en.wikipedia.org/wiki/Prokaryotic_small_ribosomal_subunit; https://en.wikipedia.org/wiki/Rhinoscleroma' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - The primary mechanism of action of amikacin is the same as that for all aminoglycosides. - It binds to bacterial 30S ribosomal subunits and interferes with mRNA binding - and tRNA acceptor sites, interfering with bacterial growth. This leads to disruption - of normal protein synthesis and production of non-functional or toxic peptides. - Other actions have been postulated for drugs of this class.[Label,F1949,F1950] - Amikacin, as well as the rest of the aminoglycosides, are generally bacteriocidal - against gram-positive and gram-negative bacteria.[L4680,F1954] - - - === - - - disease: Rhinoscleroma - - drug: Amikacin - - ' -- completion: 'disease: Menorrhagia - - drug: Tranexamic acid - - mechanism_links: Tranexamic Acid - negatively regulates - plasminogen (human); - plasminogen (human) - positively regulates - fibrinolysis; Tranexamic Acid - decreases - activity of - Fibrinolysin; Fibrinolysin - positively regulates - fibrinolysis; - fibrinolysis - correlated with - HP:0001892; HP:0001892 - positively correlated - with - Menorrhagia - - references: https://go.drugbank.com/drugs/DB00302#mechanism-of-action; https://en.wikipedia.org/wiki/Tranexamic_acid#Mechanism_of_action' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Tranexamic acid competitively inhibits activation of plasminogen (via binding - to the kringle domain), thereby reducing conversion of plasminogen to plasmin - (fibrinolysin), an enzyme that degrades fibrin clots, fibrinogen, and other plasma - proteins, including the procoagulant factors V and VIII. Tranexamic acid also - directly inhibits plasmin activity, but higher doses are required than are needed - to reduce plasmin formation. - - - === - - - disease: Menorrhagia - - drug: Tranexamic acid - - ' -- completion: 'disease: Urticaria - - drug: Methdilazine - - mechanism_links: methdilazine - decreases activity of - histamine H1 receptor - (human); histamine H1 receptor (human) - positively regulates - histamine receptor - activity; histamine receptor activity - participates in - histamine secretion - involved in inflammatory response; histamine secretion involved in inflammatory - response - positively correlated with - Urticaria - - references: https://go.drugbank.com/drugs/DB00902' - prompt: 'From the text below, extract the following entities in the following format: - - - disease: - - drug: - - mechanism_links: - - - - Text: - - Methdilazine binds to the histamine H<sub>1</sub> receptor. This blocks - the action of endogenous histamine, which subsequently leads to temporary relief - of the negative symptoms brought on by histamine. - - - === - - - disease: Urticaria - - drug: Methdilazine - - ' -template: drug.DrugMechanism diff --git a/tests/output/treatment-schiz.pickle b/tests/output/treatment-schiz.pickle deleted file mode 100644 index da37e5bda..000000000 Binary files a/tests/output/treatment-schiz.pickle and /dev/null differ diff --git a/tests/output/treatment-schiz.yaml b/tests/output/treatment-schiz.yaml deleted file mode 100644 index 77d817e21..000000000 --- a/tests/output/treatment-schiz.yaml +++ /dev/null @@ -1,110 +0,0 @@ -input_id: /Users/cjm/repos/ontogpt/tests/input/cases/treatment-schiz.txt -input_text: "According to the American Psychiatric Association, second-generation\ - \ (atypical) antipsychotics (SGAs)\u2014with the exception of clozapine\u2014are\ - \ the agents of choice for first-line treatment of schizophrenia.16,25 Clozapine\ - \ is not recommended because of its risk of agranulocytosis.2 SGAs are usually preferred\ - \ over first-generation (typical) antipsychotics (FGAs) because they are associated\ - \ with fewer extrapyramidal symptoms.2 However, SGAs tend to have metabolic side\ - \ effects, such as weight gain, hyperlipidemia, and diabetes mellitus.26 These adverse\ - \ effects can contribute to the increased risk of cardiovascular mortality observed\ - \ in schizophrenia patients.26\n\nThe Texas Medication Algorithm Project (TMAP)\ - \ has provided a six-stage pharmacotherapeutic algorithm for the treatment of schizophrenia.\ - \ Stage 1 is first-line monotherapy with an SGA. If the patient shows little or\ - \ no response, he or she should proceed to stage 2, which consists of monotherapy\ - \ with either another SGA or an FGA. If there is still no response, the patient\ - \ should move to stage 3, which consists of clozapine monotherapy with monitoring\ - \ of the white blood cell (WBC) count.24 If agranulocytosis occurs, clozapine should\ - \ be discontinued. If stage-3 therapy fails to elicit a response, the patient should\ - \ proceed to stage 4, which combines clozapine with an FGA, an SGA, or electroconvulsive\ - \ therapy (ECT).24 If the patient still shows no response to treatment, stage 5\ - \ calls for monotherapy with an FGA or an SGA that has not been tried.24 Finally,\ - \ if stage 5 treatment is unsuccessful, stage 6 consists of combination therapy\ - \ with an SGA, an FGA, ECT, and/or a mood stabilizer." -raw_completion_output: "\ndisease: Schizophrenia \ndrugs: Second-generation (atypical)\ - \ antipsychotics; Clozapine; First-generation (typical) antipsychotics; \ntreatments:\ - \ Monotherapy with an SGA; Monotherapy with either another SGA or an FGA; Clozapine\ - \ monotherapy; Combining clozapine with an FGA, an SGA, or electroconvulsive therapy;\ - \ Monotherapy with an FGA or an SGA that has not been tried; Combination therapy\ - \ with an SGA, an FGA, electroconvulsive therapy, and/or a mood stabilizer.\ncontraindications:\ - \ Clozapine \ntreatment_mechanisms: \ntreatment_efficacies: \ntreatment_adverse_effects:\ - \ Clozapine*Agranulocytosis; SGAs*Weight gain; Hyperlipidemia; Diabetes mellitus" -prompt: 'Split the following piece of text into fields in the following format: - - - treatment: - - adverse_effects: - - - - Text: - - Diabetes mellitus - - - === - - - ' -extracted_object: - disease: MONDO:0005090 - drugs: - - AUTO:Second-generation%20%28atypical%29%20antipsychotics - - CHEBI:3766 - - AUTO:First-generation%20%28typical%29%20antipsychotics - treatments: - - AUTO:Monotherapy%20with%20an%20SGA - - AUTO:Monotherapy%20with%20either%20another%20SGA%20or%20an%20FGA - - AUTO:Clozapine%20monotherapy - - AUTO:Combining%20clozapine%20with%20an%20FGA%2C%20an%20SGA%2C%20or%20electroconvulsive%20therapy - - AUTO:Monotherapy%20with%20an%20FGA%20or%20an%20SGA%20that%20has%20not%20been%20tried - - AUTO:Combination%20therapy%20with%20an%20SGA%2C%20an%20FGA%2C%20electroconvulsive%20therapy%2C%20and/or%20a%20mood%20stabilizer. - contraindications: - - NCIT:C28936 - treatment_adverse_effects: - - treatment: NCIT:C28936 - adverse_effects: - - HP:0012234 - - treatment: NCIT:C87122 - adverse_effects: - - HP:0004324 - - treatment: NCIT:C34707 - adverse_effects: - - NCIT:C18902 - - treatment: HP:0000819 -named_entities: -- id: MONDO:0005090 - label: Schizophrenia -- id: AUTO:Second-generation%20%28atypical%29%20antipsychotics - label: Second-generation (atypical) antipsychotics -- id: CHEBI:3766 - label: Clozapine -- id: AUTO:First-generation%20%28typical%29%20antipsychotics - label: First-generation (typical) antipsychotics -- id: AUTO:Monotherapy%20with%20an%20SGA - label: Monotherapy with an SGA -- id: AUTO:Monotherapy%20with%20either%20another%20SGA%20or%20an%20FGA - label: Monotherapy with either another SGA or an FGA -- id: AUTO:Clozapine%20monotherapy - label: Clozapine monotherapy -- id: AUTO:Combining%20clozapine%20with%20an%20FGA%2C%20an%20SGA%2C%20or%20electroconvulsive%20therapy - label: Combining clozapine with an FGA, an SGA, or electroconvulsive therapy -- id: AUTO:Monotherapy%20with%20an%20FGA%20or%20an%20SGA%20that%20has%20not%20been%20tried - label: Monotherapy with an FGA or an SGA that has not been tried -- id: AUTO:Combination%20therapy%20with%20an%20SGA%2C%20an%20FGA%2C%20electroconvulsive%20therapy%2C%20and/or%20a%20mood%20stabilizer. - label: Combination therapy with an SGA, an FGA, electroconvulsive therapy, and/or - a mood stabilizer. -- id: NCIT:C28936 - label: Clozapine -- id: HP:0012234 - label: Agranulocytosis -- id: NCIT:C87122 - label: SGAs -- id: HP:0004324 - label: Weight gain -- id: NCIT:C34707 - label: Hyperlipidemia -- id: NCIT:C18902 - label: N/A -- id: HP:0000819 - label: Diabetes mellitus diff --git a/tests/output/unit_test_cache.db b/tests/output/unit_test_cache.db deleted file mode 100644 index 100db9e29..000000000 Binary files a/tests/output/unit_test_cache.db and /dev/null differ diff --git a/tests/unit/test_clients/__init__.py b/tests/unit/test_clients/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/unit/test_clients/test_pubmed_client_unit.py b/tests/unit/test_clients/test_pubmed_client_unit.py deleted file mode 100644 index a6afaa253..000000000 --- a/tests/unit/test_clients/test_pubmed_client_unit.py +++ /dev/null @@ -1,23 +0,0 @@ -"""PubMed client tests.""" -import unittest - -from talisman.clients import PubmedClient - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.client = PubmedClient() - - def test_lookup(self): - """Test PMID lookup.""" - text = self.client.text("PMID:28449677") - print(text) - - def test_search(self): - """Test PMID search.""" - print("Testing...") - results = list(self.client.search("Long covid", ["review", "treatment", "therapies"])) - print(results) diff --git a/tests/unit/test_clients/test_unit_openai_client.py b/tests/unit/test_clients/test_unit_openai_client.py deleted file mode 100644 index b6a7c08a0..000000000 --- a/tests/unit/test_clients/test_unit_openai_client.py +++ /dev/null @@ -1,47 +0,0 @@ -"""Open AI client tests.""" -import re -import unittest - -import yaml - -from talisman.clients.openai_client import OpenAIClient -from tests import PROMPTS_FILE -from tests.unit import UNIT_CACHE_DB - - -class TestCompletion(unittest.TestCase): - """Test annotation.""" - - def _client(self, engine: str) -> OpenAIClient: - # TODO: use a mock - # for now we have a pseudo-mock test; the test uses cached responses - # in UNIT_CACHE_DB. - # if the test changes (e.g. a new prompt is added) then - # 1. temporarily remove the setting for api_key (it will be set from your env) - # 2. run the test - # 3. commit the new cache db - client = OpenAIClient( - model=engine, - api_key="fake", - cache_db_path=UNIT_CACHE_DB, - ) - return client - - def test_all_prompts(self): - """Test all prompts.""" - prompt_doc = yaml.safe_load(open(PROMPTS_FILE)) - default_engine = prompt_doc.get("default_engine", "gpt-3.5-turbo") - for prompt in prompt_doc["prompts"]: - prompt_text = prompt["prompt"] - if not isinstance(prompt_text, str): - prompt_text = yaml.dump(prompt_text) - engine = prompt.get("engine", default_engine) - client = self._client(engine) - pre_prompt = prompt.get("pre_prompt", "") - prompt_text = "".join([pre_prompt, prompt_text]) - print(f"## Testing prompt [{engine}: [{len(prompt_text)}] {prompt_text}") - ann = client.complete(prompt_text) - print(f"## Response: len={len(ann)}") - print(ann) - for expected in prompt.get("expected", []): - self.assertTrue(re.search(expected, ann, re.IGNORECASE)) diff --git a/tests/unit/test_converters/__init__.py b/tests/unit/test_converters/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/unit/test_converters/test_ontology_converter.py b/tests/unit/test_converters/test_ontology_converter.py deleted file mode 100644 index 44662286e..000000000 --- a/tests/unit/test_converters/test_ontology_converter.py +++ /dev/null @@ -1,63 +0,0 @@ -"""Core tests.""" -import logging -import unittest - -import yaml -from oaklib import get_implementation_from_shorthand -from oaklib.datamodels.vocabulary import IS_A, PART_OF -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from talisman.converters.ontology_converter import OntologyConverter -from talisman.engines import halo_engine -from talisman.io.yaml_wrapper import dump_minimal_yaml -from tests import INPUT_DIR, OUTPUT_DIR - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" -TEST_ONTOLOGY_HALO = INPUT_DIR / "go-nucleus.halo.yaml" -TEST_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.halo.yaml" -HALLUCINATED_ONTOLOGY_OUTPUT = OUTPUT_DIR / "go-nucleus.hallucinated.halo.yaml" - -logger = logging.getLogger(halo_engine.__name__) -logger.setLevel(level=logging.INFO) - - -class TestOntologyConverter(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up.""" - self.adapter = get_implementation_from_shorthand(str(TEST_ONTOLOGY_OAK)) - self.converter = OntologyConverter(self.adapter) - - def test_ontology_from_obograph(self): - """Test ontology from obograph.""" - oi = self.adapter - if not isinstance(oi, OboGraphInterface): - raise ValueError("Not an OboGraphInterface") - graph = oi.as_obograph() - converter = self.converter - ontology = converter.from_obograph(graph) - # print(yaml.dump(ontology.dict())) - [nucleus] = [x for x in ontology.elements if x.name == "Nucleus"] - self.assertCountEqual(["NuclearEnvelope", "NuclearMembrane"], nucleus.parts) - self.assertCountEqual(["IntracellularMembrane-boundedOrganelle"], nucleus.subclass_of) - self.assertCountEqual(["cell nucleus", "horsetail nucleus"], nucleus.synonyms) - self.assertIn("A membrane-bounded organelle", nucleus.description) - - def test_extract_seed_ontology(self): - """Test extract seed ontology.""" - converter = self.converter - preds = [IS_A, PART_OF] - ontology = converter.extract_seed_ontology( - ["GO:0031965", "GO:0005635", "GO:0006793"], preds - ) - [nucleus] = [x for x in ontology.elements if x.name == "Nucleus"] - self.assertCountEqual(["NuclearEnvelope", "NuclearMembrane"], nucleus.parts) - self.assertCountEqual(["IntracellularMembrane-boundedOrganelle"], nucleus.subclass_of) - self.assertCountEqual(["cell nucleus", "horsetail nucleus"], nucleus.synonyms) - self.assertIn("A membrane-bounded organelle", nucleus.description) - [nm] = [x for x in ontology.elements if x.name == "NuclearMembrane"] - print(yaml.dump(nm.dict())) - self.assertEqual("Membrane and part of some Nucleus", nm.equivalent_to) - with open(TEST_ONTOLOGY_OUTPUT, "w") as f: - f.write(dump_minimal_yaml(ontology)) diff --git a/tests/unit/test_exporters/__init__.py b/tests/unit/test_exporters/__init__.py deleted file mode 100644 index 3cd856bdd..000000000 --- a/tests/unit/test_exporters/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -from tests import INPUT_DIR - -TEST_PICKLED_RESULTS = str(INPUT_DIR / "recipe-spaghetti.pickle") diff --git a/tests/unit/test_exporters/test_html_exporter.py b/tests/unit/test_exporters/test_html_exporter.py deleted file mode 100644 index b0a43012d..000000000 --- a/tests/unit/test_exporters/test_html_exporter.py +++ /dev/null @@ -1,23 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from talisman.io.html_exporter import HTMLExporter -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExportHTML(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = HTMLExporter() - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - - def test_export(self): - """Test export.""" - with open(str(OUTPUT_DIR / "test-output.html"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f) diff --git a/tests/unit/test_exporters/test_markdown_exporter.py b/tests/unit/test_exporters/test_markdown_exporter.py deleted file mode 100644 index a04591960..000000000 --- a/tests/unit/test_exporters/test_markdown_exporter.py +++ /dev/null @@ -1,24 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from talisman.io.markdown_exporter import MarkdownExporter -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExport(unittest.TestCase): - """Test annotation.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = MarkdownExporter() - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - # print(yaml.dump(self.extraction_result.dict())) - - def test_export(self): - """Test export.""" - with open(str(OUTPUT_DIR / "test-output.md"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f) diff --git a/tests/unit/test_exporters/test_owl_exporter.py b/tests/unit/test_exporters/test_owl_exporter.py deleted file mode 100644 index 329cef28d..000000000 --- a/tests/unit/test_exporters/test_owl_exporter.py +++ /dev/null @@ -1,34 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from linkml_runtime import SchemaView - -from talisman.io.owl_exporter import OWLExporter -from talisman.templates import PATH_TO_TEMPLATES -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExportOWL(unittest.TestCase): - """Test exporting from pre-made results to OWL.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = OWLExporter() - self.schemaview = SchemaView(str(PATH_TO_TEMPLATES / "recipe.yaml")) - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - - def test_export(self): - """Test export.""" - print(f"URL={self.extraction_result.extracted_object.url}") - print(f"Label={self.extraction_result.extracted_object.label}") - with open(str(OUTPUT_DIR / "recipe-spaghetti.owl"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f, self.schemaview, id_value="AUTO:_ROOT") - - def test_export2(self): - """Test export.""" - with open(str(OUTPUT_DIR / "recipe-palak-paneer.owl"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f, self.schemaview, id_value="AUTO:_ROOT") diff --git a/tests/unit/test_exporters/test_rdf_exporter.py b/tests/unit/test_exporters/test_rdf_exporter.py deleted file mode 100644 index 361833b03..000000000 --- a/tests/unit/test_exporters/test_rdf_exporter.py +++ /dev/null @@ -1,27 +0,0 @@ -"""Core tests.""" -import pickle -import unittest - -from linkml_runtime import SchemaView - -from talisman.io.rdf_exporter import RDFExporter -from talisman.templates import PATH_TO_TEMPLATES -from tests import OUTPUT_DIR -from tests.unit.test_exporters import TEST_PICKLED_RESULTS - - -@unittest.skip("Not yet fully compatible with linkml exporters and test fixtures") -class TestExportRDF(unittest.TestCase): - """Test RDF export.""" - - def setUp(self) -> None: - """Set up.""" - self.exporter = RDFExporter() - self.schemaview = SchemaView(str(PATH_TO_TEMPLATES / "recipe.yaml")) - with open(TEST_PICKLED_RESULTS, "rb") as f: - self.extraction_result = pickle.load(f) - - def test_export(self): - """Test export.""" - with open(str(OUTPUT_DIR / "test-output.ttl"), "w", encoding="utf-8") as f: - self.exporter.export(self.extraction_result, f, self.schemaview) diff --git a/tests/unit/test_ontex/__init__.py b/tests/unit/test_ontex/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/tests/unit/test_ontex/test_extract.py b/tests/unit/test_ontex/test_extract.py deleted file mode 100644 index 69b1a228a..000000000 --- a/tests/unit/test_ontex/test_extract.py +++ /dev/null @@ -1,176 +0,0 @@ -"""Core tests.""" -import csv -import logging -import unittest -from typing import Iterator, List, Tuple - -import yaml -from oaklib import get_adapter -from oaklib.datamodels.vocabulary import IS_A, PART_OF -from oaklib.interfaces.obograph_interface import OboGraphInterface - -from talisman.io.yaml_wrapper import dump_minimal_yaml -from talisman.ontex import extractor -from talisman.ontex.extractor import OntologyExtractor, Task, TaskCollection -from tests import ( - CELLULAR_ANATOMICAL_ENTITY, - ENVELOPE, - FUNGI, - IMBO, - INPUT_DIR, - INTRACELLULAR_ORGANELLE, - MEMBRANE_BOUNDED_ORGANELLE, - NUCLEAR_ENVELOPE, - NUCLEAR_MEMBRANE, - NUCLEUS, - ORGANELLE, - OUTPUT_DIR, - VACUOLE, -) - -TEST_ONTOLOGY_OAK = INPUT_DIR / "go-nucleus.db" -TEST_ONTOLOGY_ABOX = INPUT_DIR / "fhkb.db" - - -logger = logging.getLogger(extractor.__name__) -logger.setLevel(level=logging.INFO) - -IS_ANCESTOR_OF = "fhkb:isAncestorOf" -HAS_ANCESTOR = "fhkb:hasAncestor" -HAS_PARENT = "fhkb:hasParent" -IS_PARENT_OF = "fhkb:isParentOf" -HAS_FATHER = "fhkb:hasFather" -HAS_MOTHER = "fhkb:hasMother" -HAS_PARENT = "fhkb:hasParent" -HAS_SIBLING = "fhkb:hasSibling" -HAS_BROTHER = "fhkb:hasBrother" -HAS_SISTER = "fhkb:hasSister" - - -class TestOntologyExtractor(unittest.TestCase): - """Test ability to convert from OAK to native HALO form.""" - - def setUp(self) -> None: - """Set up.""" - self.adapter = get_adapter(str(TEST_ONTOLOGY_OAK)) - self.abox_adapter = get_adapter(str(TEST_ONTOLOGY_ABOX)) - if not isinstance(self.adapter, OboGraphInterface): - raise ValueError("Not an OboGraphInterface") - self.extractor = OntologyExtractor(adapter=self.adapter) - self.abox_extractor = OntologyExtractor(adapter=self.abox_adapter) - self.abox_extractor.query_predicates = [HAS_ANCESTOR, HAS_SIBLING] - - def cases(self) -> Iterator[Tuple[Task, List[str]]]: - extractor = self.extractor - # yield extractor.extract_indirect_superclasses_task(select_random=True), None - yield extractor.extract_transitive_superclasses_task( - subclass=NUCLEUS, siblings=[VACUOLE], roots=[ORGANELLE] - ), [ORGANELLE, IMBO, INTRACELLULAR_ORGANELLE, MEMBRANE_BOUNDED_ORGANELLE] - yield extractor.extract_indirect_superclasses_task( - subclass=NUCLEUS, siblings=[VACUOLE], roots=[ORGANELLE] - ), [ORGANELLE, INTRACELLULAR_ORGANELLE, MEMBRANE_BOUNDED_ORGANELLE] - yield extractor.extract_most_recent_common_subsumers_task( - subclass1=NUCLEUS, subclass2=VACUOLE, siblings=[NUCLEAR_MEMBRANE], roots=[] - ), [IMBO] - yield extractor.extract_incoherent_ontology_task( - incoherents=[NUCLEUS], - siblings=[VACUOLE], - disjoints=[(ORGANELLE, ENVELOPE)], - spiked_relationships=[(NUCLEUS, IS_A, NUCLEAR_MEMBRANE)], - roots=[CELLULAR_ANATOMICAL_ENTITY], - ), [NUCLEUS] - yield extractor.extract_subclass_of_expression_task( - superclass=NUCLEUS, - predicate=PART_OF, - siblings=[VACUOLE], - ), [NUCLEAR_MEMBRANE, NUCLEAR_ENVELOPE] - yield extractor.extract_subclass_of_expression_task( - superclass=IMBO, - predicate=PART_OF, - siblings=[FUNGI], - ), [NUCLEAR_MEMBRANE, NUCLEAR_ENVELOPE] - - def test_extract(self): - """Test extract tasks.""" - extractor = self.extractor - for task, expected in self.cases(): - if not task.ontology.axioms: - raise ValueError(f"Task {task} has no axioms") - print(yaml.dump(task.dict(), sort_keys=False)) - answer_texts = [a.text for a in task.answers] - if expected is not None: - self.assertCountEqual(answer_texts, [extractor._name(x) for x in expected]) - - @unittest.skip("Non-deterministic") - def test_random_taxon_constraints(self): - """Test extract random tasks.""" - extractor = self.extractor - task = extractor.extract_taxon_constraint_task(select_random=True, never_in=True) - print(dump_minimal_yaml(task)) - - @unittest.skip("Non-deterministic") - def test_random(self): - """Test extract random tasks.""" - extractor = self.extractor - abox_extractor = self.abox_extractor - abox_tc = abox_extractor.create_random_tasks(20, abox=True) - tc = extractor.create_random_tasks(20, abox=False) - tc.tasks.extend(abox_tc.tasks) - for task in tc.tasks: - if not task.answers: - print(f"Task {task} has no answers") - # raise ValueError(f"Task {task} has no answers") - if not task.ontology.axioms: - raise ValueError(f"Task {task} has no axioms") - # raise ValueError(f"Task {task} has no axioms") - path = OUTPUT_DIR / "random-reasoner-tasks.yaml" - with open(path, "w") as f: - f.write(dump_minimal_yaml(tc)) - tc = TaskCollection.load(path) - task_types = {type(obj) for obj in tc.tasks} - print(len(tc.tasks)) - print(task_types) - # increase this every time you add a new task type - self.assertEqual(len(task_types), 7) - - @unittest.skip("Non-deterministic") - def test_random_obfuscated(self): - extractor = self.extractor - extractor.obfuscate = True - abox_extractor = self.abox_extractor - abox_extractor.obfuscate = True - abox_tc = abox_extractor.create_random_tasks(20, abox=True) - tc = extractor.create_random_tasks(20, abox=False) - # merge - tc.tasks.extend(abox_tc.tasks) - for task in tc.tasks: - if not task.answers: - print(f"Task {task} has no answers") - # raise ValueError(f"Task {task} has no answers") - if not task.ontology.axioms: - raise ValueError(f"Task {task} has no axioms") - # raise ValueError(f"Task {task} has no axioms") - path = OUTPUT_DIR / "obfuscated-reasoner-tasks.yaml" - with open(path, "w") as f: - f.write(dump_minimal_yaml(tc)) - tc = TaskCollection.load(path) - task_types = {type(obj) for obj in tc.tasks} - print(len(tc.tasks)) - print(task_types) - # increase this every time you add a new task type - self.assertEqual(len(task_types), 6) - self.assertGreater(len(tc.obfuscated_curie_map.keys()), 20) - - def test_introspect(self): - """Test introspection.""" - root_class = Task - with open(OUTPUT_DIR / "task-classes.tsv", "w") as f: - writer = csv.DictWriter(f, fieldnames=["code", "task", "description"], delimiter="\t") - writer.writeheader() - for subclass in root_class.__subclasses__(): - row = { - "code": subclass._code, - "task": subclass.__name__, - "description": subclass.__doc__.replace("\n", " ").strip(), - } - writer.writerow(row) diff --git a/tests/unit/test_utils/test_yaml_wrapper.py b/tests/unit/test_utils/test_yaml_wrapper.py deleted file mode 100644 index 1d482be79..000000000 --- a/tests/unit/test_utils/test_yaml_wrapper.py +++ /dev/null @@ -1,39 +0,0 @@ -"""Tests YAML utils.""" -import io -import unittest - -from ruamel.yaml import YAML, RoundTripRepresenter - - -def repr_str(dumper: RoundTripRepresenter, data: str): - if "\n" in data: - return dumper.represent_scalar("tag:yaml.org,2002:str", data, style="|") - return dumper.represent_scalar("tag:yaml.org,2002:str", data) - - -class TestYAML(unittest.TestCase): - def test_dump_load(self): - # previous versions of ruamel.yaml would generate unparsable yaml - # for certain combinations of whitespace and embedded yaml tokens - cases = [ - "\nfoo: bar", - " \nfoo: bar", - " \n foo: bar", - " \n foo: bar\n{}", - " \n foo: bar\n{} ", - " \n foo: bar\n{}\n|\n{", - ] - for case in cases: - obj = {"a": case} - # yaml = YAML(typ="safe") - yaml = YAML() - yaml.representer.add_representer(str, repr_str) - yaml.default_flow_style = False - yaml.indent(sequence=4, offset=2) - file = io.StringIO() - yaml.dump(obj, file) - ys = file.getvalue() - # print(ys) - yaml = YAML() - r = yaml.load(ys) - self.assertEqual(r, obj)