ontogpt
LLM-based ontological extraction tools, including SPIRES
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Download Latest Version (.zip)- deploy-docs.yml
- pypi-publish.yml
- qc.yml
- custom.md
- evaluations.md
- functions.md
- index.md
- operation.md
- owl_exports.md
- setup.md
- start_with_owl.md
- troubleshooting.md
- ontogpt_logo_2.jpg
- ontogpt_logo_2.svg
- ontogpt_logo_3.jpg
- spires_logo.png
- spires_logo.svg
- Enrichment-Results-Analysis.ipynb
- parse_msigdb.ipynb
- BioEPIC_demo.ipynb
- output1.yaml
- output2.yaml
- output3.yaml
- Quick-Examples.ipynb
- text.txt
- text2.txt
- __init__.py
- llm_client.py
- openai_client.py
- pubmed_client.py
- soup_client.py
- wikipedia_client.py
- synonymizer-conf.yaml
- __init__.py
- ontology_converter.py
- __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
- CDR_TestSet.BioC.xml.gz
- CDR_TrainSet.BioC.xml.gz
- synonyms.yaml
- __init__.py
- eval_ctd.py
- eval_ctd_ner.py
- drugmechdb.py
- drugmechdb.yaml
- __init__.py
- eval_drugmechdb.py
- eval_go.py
- __init__.py
- eval_hpoa.py
- 10338374.txt
- 17653185.txt
- 18253950.txt
- 24104886.txt
- 28846760.txt
- 29285689.txt
- 29441064.txt
- 31767987.txt
- PMC4961083.txt
- PMC6386158.txt
- PMC7003169.txt
- 10338374_smoking.txt
- PMC6386158_review.txt
- PMC6386158_review_fig2_legend.txt
- PMC6386158_review_fig2_legend.yaml
- 10338374_nicotine.txt
- PMC6386158_fig2_legend.txt~
- run.sh
- run.sh~
- test.txt
- test2.txt
- test3.txt
- 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
- __init__.py
- eval_maxo.py
- __init__.py
- evaluation_engine.py
- resolver.py
- __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
- __init__.py
- extractor.py
- __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
- __init__.py
- eval-mapping.jinja2
- __init__.py
- phenopacket.jinja2
- __init__.py
- generic.jinja2
- __init__.py
- reasoning.jinja2
- connections.jinja2
- __init__.py
- __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
- aop.py
- aop.yaml
- biological_process.py
- biological_process.yaml
- biomed_terminology.py
- biomed_terminology.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
- __init__.py
- clinical_cases.py
- model_utils.py
- multilingual.py
- output_parser.py
- output_parser_bulleted.py
- parse_utils.py
- pymupdf_helpers.py
- form.html
- results.html
- loading.gif
- __init__.py
- main.py
- __init__.py
- cli.py
- 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
- biological-process-cysteine-biosynthesis.yaml
- drug-mechanisms-001.yaml
- ontology-class-ncit-001.yaml
- reactions-001.yaml
- nedema-prompt.yaml
- prompts.yaml
- terms.rq
- training-ctd-001.yaml
- training-drugmechdb-001.jsonl
- training-drugmechdb-001.yaml
- training-mendelian-disease-001.jsonl
- training-mendelian-disease-001.yaml
- 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
- Guo-2017-EXTL3-Patient_1.json
- industry-ontology-seed.yaml
- inter-organism.yaml
- mondo-exact-ncit.sssom.tsv
- recipe-spaghetti.pickle
- recipe-urls.csv
- test.hpoa.tsv
- test_sample.hpoa.tsv
- test_cli.py
- __init__.py
- test_llmclient.py
- test_pubmed_client.py
- __init__.py
- test_eval_ctd.py
- test_eval_drugmechdb.py
- test_eval_go.py
- test_eval_hpoa.py
- __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
- __init__.py
- drug-DB00316-moa.yaml
- recipe-spaghetti.html
- recipe-spaghetti.md
- recipe-spaghetti.yaml
- treatment-schiz.html
- treatment-schiz.md
- treatment-schiz.yaml
- treatment.DiseaseTreatmentSummary-search-covid_19.yaml
- recipe-all-merged.owl
- 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
- reaction-20657015.pickle
- reaction-20657015.yaml
- reaction-21290071.pickle
- reaction-21290071.yaml
- README.md
- reasoner-basic-gpt-4o.tsv
- reasoner-basic-gpt-4o.yaml
- reasoner-chain-of-thought-gpt-4o.tsv
- reasoner-chain-of-thought-gpt-4o.yaml
- reasoner-explanation-gpt-4o.tsv
- reasoner-explanation-gpt-4o.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
- __init__.py
- test_llmclient.py
- test_pubmed_client_unit.py
- __init__.py
- test_ontology_converter.py
- __init__.py
- test_csv_exporter.py
- test_html_exporter.py
- test_markdown_exporter.py
- test_owl_exporter.py
- test_rdf_exporter.py
- __init__.py
- test_extract.py
- __init__.py
- test_io_utils.py
- test_parse_utils.py
- test_yaml_wrapper.py
- __init__.py
- test_unit_cli.py
- __init__.py
- ctd-train2obo.pl
- ctd-train2tsv.pl
- ctd-train2yaml.pl
- dump-omim2pmid.pl
- filter-hpoa.pl
- .cruft.json
- .gitignore
- CITATION.cff
- LICENSE
- Makefile
- MANIFEST.in
- mkdocs.yml
- pyproject.toml
- README.md
- tox.ini
- uv.lock
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