├── .cruft.json ├── .github └── workflows │ ├── deploy-docs.yml │ ├── pypi-publish.yml │ └── qc.yml ├── .gitignore ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── docs ├── custom.md ├── evaluations.md ├── functions.md ├── index.md ├── operation.md ├── owl_exports.md ├── setup.md ├── start_with_owl.md └── troubleshooting.md ├── images ├── ontogpt_logo_2.jpg ├── ontogpt_logo_2.svg ├── ontogpt_logo_3.jpg ├── spires_logo.png └── spires_logo.svg ├── mkdocs.yml ├── notebooks ├── BioEPIC_demo.ipynb ├── Quick-Examples.ipynb ├── old │ ├── Enrichment-Results-Analysis.ipynb │ └── parse_msigdb.ipynb ├── output1.yaml ├── output2.yaml ├── output3.yaml ├── text.txt └── text2.txt ├── pyproject.toml ├── src └── ontogpt │ ├── __init__.py │ ├── cli.py │ ├── clients │ ├── __init__.py │ ├── llm_client.py │ ├── pubmed_client.py │ ├── soup_client.py │ └── wikipedia_client.py │ ├── conf │ └── synonymizer-conf.yaml │ ├── converters │ ├── __init__.py │ └── ontology_converter.py │ ├── engines │ ├── __init__.py │ ├── embedding_similarity_engine.py │ ├── generic_engine.py │ ├── halo_engine.py │ ├── knowledge_engine.py │ ├── mapping_engine.py │ ├── pheno_engine.py │ ├── reasoner_engine.py │ ├── resolver.py │ ├── spires_engine.py │ ├── synonym_engine.py │ └── topic_classifier_engine.py │ ├── evaluation │ ├── __init__.py │ ├── ctd │ │ ├── __init__.py │ │ ├── database │ │ │ ├── CDR_TestSet.BioC.xml.gz │ │ │ ├── CDR_TrainSet.BioC.xml.gz │ │ │ └── synonyms.yaml │ │ ├── eval_ctd.py │ │ └── eval_ctd_ner.py │ ├── drugmechdb │ │ ├── __init__.py │ │ ├── datamodel │ │ │ ├── drugmechdb.py │ │ │ └── drugmechdb.yaml │ │ └── eval_drugmechdb.py │ ├── evaluation_engine.py │ ├── go │ │ └── eval_go.py │ ├── hpoa │ │ ├── __init__.py │ │ └── eval_hpoa.py │ ├── ibd │ │ ├── 10338374_nicotine.txt │ │ ├── Abstracts │ │ │ ├── 10338374.txt │ │ │ ├── 17653185.txt │ │ │ ├── 18253950.txt │ │ │ ├── 24104886.txt │ │ │ ├── 28846760.txt │ │ │ ├── 29285689.txt │ │ │ ├── 29441064.txt │ │ │ ├── 31767987.txt │ │ │ ├── PMC4961083.txt │ │ │ ├── PMC6386158.txt │ │ │ └── PMC7003169.txt │ │ ├── PMC6386158_fig2_legend.txt~ │ │ ├── run.sh │ │ ├── run.sh~ │ │ └── text_data │ │ │ ├── 10338374_smoking.txt │ │ │ ├── PMC6386158_review.txt │ │ │ ├── PMC6386158_review_fig2_legend.txt │ │ │ └── PMC6386158_review_fig2_legend.yaml │ ├── kidney │ │ ├── test.txt │ │ ├── test2.txt │ │ └── test3.txt │ ├── maxo │ │ ├── __init__.py │ │ ├── eval_maxo.py │ │ └── test_cases │ │ │ ├── maxo_case_12958596.yaml │ │ │ ├── maxo_case_20301368.yaml │ │ │ ├── maxo_case_20301450.yaml │ │ │ ├── maxo_case_20301519.yaml │ │ │ ├── maxo_case_20301527.yaml │ │ │ ├── maxo_case_20301572.yaml │ │ │ ├── maxo_case_20301644.yaml │ │ │ ├── maxo_case_20301675.yaml │ │ │ ├── maxo_case_20301765.yaml │ │ │ ├── maxo_case_2063868.yaml │ │ │ ├── maxo_case_26110198.yaml │ │ │ ├── maxo_case_27077170.yaml │ │ │ ├── maxo_case_28406602.yaml │ │ │ ├── maxo_case_29478819.yaml │ │ │ ├── maxo_case_30488337.yaml │ │ │ ├── maxo_case_36977302.yaml │ │ │ └── maxo_case_9543069.yaml │ └── resolver.py │ ├── io │ ├── __init__.py │ ├── csv_exporter.py │ ├── csv_wrapper.py │ ├── exporter.py │ ├── html_exporter.py │ ├── json_wrapper.py │ ├── markdown_exporter.py │ ├── owl_exporter.py │ ├── rdf_exporter.py │ ├── template_loader.py │ ├── utils.py │ └── yaml_wrapper.py │ ├── ontex │ ├── __init__.py │ └── extractor.py │ ├── prompts │ ├── __init__.py │ ├── enrichment │ │ ├── __init__.py │ │ ├── gene_set_summarization.jinja2 │ │ ├── gene_set_summarization_with_p_values.jinja2 │ │ ├── gene_set_summarization_with_p_values_0.jinja2 │ │ ├── gene_set_summarization_with_p_values_1.jinja2 │ │ └── gene_set_summarization_with_p_values_2.jinja2 │ ├── mapping │ │ ├── __init__.py │ │ └── eval-mapping.jinja2 │ ├── phenopacket │ │ ├── __init__.py │ │ └── phenopacket.jinja2 │ ├── qa │ │ ├── __init__.py │ │ └── generic.jinja2 │ ├── reasoning │ │ ├── __init__.py │ │ └── reasoning.jinja2 │ └── similarity │ │ └── connections.jinja2 │ ├── templates │ ├── __init__.py │ ├── adverse_outcome_pathway.py │ ├── adverse_outcome_pathway.yaml │ ├── all_disease_grounding.py │ ├── all_disease_grounding.yaml │ ├── alzrd.py │ ├── alzrd.yaml │ ├── alzrd_section.py │ ├── alzrd_section.yaml │ ├── biological_process.py │ ├── biological_process.yaml │ ├── biotic_interaction.py │ ├── biotic_interaction.yaml │ ├── cell_type.py │ ├── cell_type.yaml │ ├── class_enrichment.py │ ├── class_enrichment.yaml │ ├── composite_disease.py │ ├── composite_disease.yaml │ ├── condition.py │ ├── condition.yaml │ ├── core.py │ ├── core.yaml │ ├── ctd.py │ ├── ctd.yaml │ ├── ctd_ner.py │ ├── ctd_ner.yaml │ ├── data_sheets_schema.py │ ├── data_sheets_schema.yaml │ ├── datasheet.py │ ├── datasheet.yaml │ ├── desiccation.py │ ├── desiccation.yaml │ ├── diagnostic_procedure.py │ ├── diagnostic_procedure.yaml │ ├── dietitian_notes.py │ ├── dietitian_notes.yaml │ ├── drug.py │ ├── drug.yaml │ ├── drug_to_disease.py │ ├── drug_to_disease.yaml │ ├── ecosim_methods.py │ ├── ecosim_methods.yaml │ ├── ecosim_simple.py │ ├── ecosim_simple.yaml │ ├── emapa_simple.py │ ├── emapa_simple.yaml │ ├── environmental_metadata.py │ ├── environmental_metadata.yaml │ ├── environmental_sample.py │ ├── environmental_sample.yaml │ ├── environmental_sample_ungrounded.py │ ├── environmental_sample_ungrounded.yaml │ ├── error_analysis.py │ ├── error_analysis.yaml │ ├── figure.py │ ├── figure.yaml │ ├── food.py │ ├── food.yaml │ ├── foodon_simple.py │ ├── foodon_simple.yaml │ ├── gene_description_term.py │ ├── gene_description_term.yaml │ ├── gene_extraction.py │ ├── gene_extraction.yaml │ ├── genesummary.py │ ├── genesummary.yaml │ ├── go_simple.py │ ├── go_simple.yaml │ ├── go_terms.py │ ├── go_terms.yaml │ ├── go_terms_relational.py │ ├── go_terms_relational.yaml │ ├── gocam.py │ ├── gocam.yaml │ ├── halo.py │ ├── halo.yaml │ ├── human_phenotype.py │ ├── human_phenotype.yaml │ ├── ibd.py │ ├── ibd.yaml │ ├── ibd_literature.py │ ├── ibd_literature.yaml │ ├── kidney.py │ ├── kidney.yaml │ ├── matrix_eval.py │ ├── matrix_eval.yaml │ ├── maxo.py │ ├── maxo.yaml │ ├── mendelian_disease.py │ ├── mendelian_disease.yaml │ ├── metabolic_process.py │ ├── metabolic_process.yaml │ ├── metagenome_study.py │ ├── metagenome_study.yaml │ ├── mic.py │ ├── mic.yaml │ ├── miro.py │ ├── miro.yaml │ ├── mondo_simple.py │ ├── mondo_simple.yaml │ ├── nmdc_schema_data.py │ ├── nmdc_schema_data.yaml │ ├── onto_usage.py │ ├── onto_usage.yaml │ ├── ontology_class.py │ ├── ontology_class.yaml │ ├── ontology_issue.py │ ├── ontology_issue.yaml │ ├── pathology.py │ ├── pathology.yaml │ ├── personinfo.py │ ├── personinfo.yaml │ ├── phenopackets.py │ ├── phenopackets.yaml │ ├── phenotype.py │ ├── phenotype.yaml │ ├── predator_prey.py │ ├── predator_prey.yaml │ ├── reaction.py │ ├── reaction.yaml │ ├── recipe.py │ ├── recipe.yaml │ ├── storms.py │ ├── storms.yaml │ ├── table_arrays.py │ ├── table_arrays.yaml │ ├── table_values.py │ ├── table_values.yaml │ ├── traits.py │ ├── traits.yaml │ ├── treatment.py │ ├── treatment.yaml │ ├── vbo_char.py │ ├── vbo_char.yaml │ ├── vbo_names.py │ └── vbo_names.yaml │ ├── utils │ ├── __init__.py │ ├── clinical_cases.py │ ├── model_utils.py │ ├── multilingual.py │ ├── output_parser.py │ ├── output_parser_bulleted.py │ ├── parse_utils.py │ └── pymupdf_helpers.py │ └── webapp │ ├── __init__.py │ ├── html │ ├── form.html │ └── results.html │ ├── main.py │ └── static │ └── loading.gif ├── tests ├── __init__.py ├── input │ ├── Guo-2017-EXTL3-Patient_1.json │ ├── cases │ │ ├── amphibian_skin.txt │ │ ├── biotic_interaction-001.txt │ │ ├── biotic_interaction-002.txt │ │ ├── biotic_interaction-003.txt │ │ ├── biotic_interaction-004.txt │ │ ├── biotic_interaction-005.txt │ │ ├── biotic_interaction-006.txt │ │ ├── biotic_interaction-007.txt │ │ ├── biotic_interaction-008.txt │ │ ├── biotic_interaction-009.txt │ │ ├── biotic_interaction-010.txt │ │ ├── biotic_interaction-011.txt │ │ ├── biotic_interaction-012.txt │ │ ├── cell-type-salivary-acinar.txt │ │ ├── dental-restoration-material-ceramic-1.txt │ │ ├── dental-restoration-material-ceramic-2.txt │ │ ├── dental-restoration-material-ceramic-composite-1.txt │ │ ├── dental-restoration-material-ceramic-composite-polymer-1.txt │ │ ├── dental-restoration-material-ceramic-composite-polymer-2.txt │ │ ├── dental-restoration-material-ceramic-composite-polymer-resin-1.txt │ │ ├── dental-restoration-material-ceramic-composite-polymer-resin-2.txt │ │ ├── dental-restoration-material-ceramic-composite-resin-1.txt │ │ ├── dental-restoration-material-composite-1.txt │ │ ├── dental-restoration-material-composite-2.txt │ │ ├── dental-restoration-material-composite-polymer-1.txt │ │ ├── dental-restoration-material-composite-resin-1.txt │ │ ├── dental-restoration-material-polymer-1.txt │ │ ├── dental-restoration-material-polymer-2.txt │ │ ├── dental-restoration-material-resin-1.txt │ │ ├── dental-restoration-material-resin-2.txt │ │ ├── drug-DB00316-moa.txt │ │ ├── environmental-metadata-1.txt │ │ ├── environmental-metadata-2.txt │ │ ├── environmental-metadata-3.txt │ │ ├── environmental-sample-hyporheic.txt │ │ ├── gocam-27929086.txt │ │ ├── gocam-33246504.txt │ │ ├── gocam-betacat.txt │ │ ├── human_smoking_China.txt │ │ ├── human_urban_green_space.txt │ │ ├── mendelian-disease-cmt2e-summary.txt │ │ ├── mendelian-disease-cmt2e.txt │ │ ├── mendelian-disease-marfan.txt │ │ ├── mendelian-disease-sly.txt │ │ ├── omim-608716.txt │ │ ├── omim-619428.txt │ │ ├── omim-620038.txt │ │ ├── reaction-20657015.txt │ │ ├── reaction-21290071.txt │ │ ├── recipe-egg-noodles.txt │ │ ├── recipe-spaghetti.txt │ │ ├── recipe-tortilla-soup.txt │ │ ├── traits-dinoflagellate.txt │ │ ├── traits-patescibacteria.txt │ │ ├── treatment-eds.txt │ │ ├── treatment-marfan.txt │ │ └── treatment-schiz.txt │ ├── dentin.txt │ ├── drug-mech-db-example.yaml │ ├── eds-output.pickle │ ├── eds-output.yaml │ ├── example-raw-output.txt │ ├── fhkb.db │ ├── fhkb.owl │ ├── genes2go.tsv.gz │ ├── go-nucleus.db │ ├── go-nucleus.halo.yaml │ ├── go-nucleus.json │ ├── industry-ontology-seed.yaml │ ├── instances │ │ ├── biological-process-cysteine-biosynthesis.yaml │ │ ├── drug-mechanisms-001.yaml │ │ ├── ontology-class-ncit-001.yaml │ │ └── reactions-001.yaml │ ├── inter-organism.yaml │ ├── mondo-exact-ncit.sssom.tsv │ ├── prompts │ │ ├── nedema-prompt.yaml │ │ └── prompts.yaml │ ├── queries │ │ └── terms.rq │ ├── recipe-spaghetti.pickle │ ├── recipe-urls.csv │ ├── test.hpoa.tsv │ ├── test_sample.hpoa.tsv │ └── training │ │ ├── training-ctd-001.yaml │ │ ├── training-drugmechdb-001.jsonl │ │ ├── training-drugmechdb-001.yaml │ │ ├── training-mendelian-disease-001.jsonl │ │ └── training-mendelian-disease-001.yaml ├── integration │ ├── __init__.py │ ├── test_cli │ │ └── test_cli.py │ ├── test_clients │ │ ├── __init__.py │ │ ├── test_llmclient.py │ │ └── test_pubmed_client.py │ ├── test_evaluation │ │ ├── __init__.py │ │ ├── test_eval_ctd.py │ │ ├── test_eval_drugmechdb.py │ │ ├── test_eval_go.py │ │ └── test_eval_hpoa.py │ └── test_knowledge_engines │ │ ├── __init__.py │ │ ├── test_cases.py │ │ ├── test_generalizations.py │ │ ├── test_halo_engine.py │ │ ├── test_mapping.py │ │ ├── test_pheno.py │ │ ├── test_reasoning.py │ │ └── test_spires_engine.py ├── output │ ├── README.md │ ├── carbohydrate-metabolism.hallucinated.halo.yaml │ ├── drug-DB00316-moa.pickle │ ├── drug-DB00316-moa.yaml │ ├── drugmechdb-normalized.yaml.gz │ ├── eds-output.html │ ├── eds-output.md │ ├── gene_requests_cache.db │ ├── generalized-drug-mechanisms-001.yaml │ ├── generalized-reactions-001.yaml │ ├── go-nucleus.hallucinated.halo.yaml │ ├── go-nucleus.halo.yaml │ ├── gocam-27929086.pickle │ ├── gocam-27929086.yaml │ ├── gocam-33246504.pickle │ ├── gocam-33246504.yaml │ ├── gocam-betacat.pickle │ ├── gocam-betacat.yaml │ ├── mendelian-disease-cmt2e-summary.pickle │ ├── mendelian-disease-cmt2e-summary.yaml │ ├── mendelian-disease-cmt2e.pickle │ ├── mendelian-disease-cmt2e.yaml │ ├── mendelian-disease-marfan.pickle │ ├── mendelian-disease-marfan.yaml │ ├── mendelian-disease-sly.pickle │ ├── mendelian-disease-sly.yaml │ ├── owl │ │ └── merged │ │ │ └── recipe-all-merged.owl │ ├── reaction-20657015.pickle │ ├── reaction-20657015.yaml │ ├── reaction-21290071.pickle │ ├── reaction-21290071.yaml │ ├── recipe-egg-noodles.pickle │ ├── recipe-egg-noodles.yaml │ ├── recipe-palak-paneer.owl │ ├── recipe-spaghetti.owl │ ├── recipe-spaghetti.pickle │ ├── recipe-spaghetti.yaml │ ├── recipe-tortilla-soup.pickle │ ├── recipe-tortilla-soup.yaml │ ├── spires-extract-spaghetti.owl │ ├── task-classes.tsv │ ├── test-output.html │ ├── test-output.md │ ├── training-drugmechdb.yaml │ ├── treatment-schiz.pickle │ ├── treatment-schiz.yaml │ └── unit_test_cache.db └── unit │ ├── __init__.py │ ├── test_clients │ ├── __init__.py │ ├── test_llmclient.py │ └── test_pubmed_client_unit.py │ ├── test_converters │ ├── __init__.py │ └── test_ontology_converter.py │ 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