├── .cruft.json ├── .github └── workflows │ ├── deploy-docs.yml │ ├── pypi-publish.yml │ └── qc.yml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── mkdocs.yml ├── poetry.lock ├── pyproject.toml ├── src └── semantic_llama │ ├── __init__.py │ ├── cli.py │ ├── clients │ ├── __init__.py │ ├── openai_client.py │ └── pubmed_client.py │ ├── engines │ ├── __init__.py │ ├── code_model_knowledge_engine.py │ ├── engine.py │ ├── resolver.py │ └── text_model_knowledge_engine.py │ ├── evaluation │ ├── __init__.py │ ├── drugmechdb │ │ ├── __init__.py │ │ ├── database │ │ │ └── drugmechdb-normalized.yaml.gz │ │ ├── datamodel │ │ │ ├── drugmechdb.py │ │ │ └── drugmechdb.yaml │ │ ├── eval_drugmechdb.py │ │ └── exemplars │ │ │ └── drugmechdb-exemplars.yaml │ ├── evaluation_engine.py │ ├── go │ │ ├── eval_go.py │ │ ├── exemplars │ │ │ └── go-chebi-exemplars.obo │ │ └── test_cases │ │ │ ├── go-chebi-2022.obo │ │ │ └── go-ids-2022.txt │ └── hpoa │ │ ├── __init__.py │ │ ├── eval_hpoa.py │ │ └── test_cases │ │ ├── omim-104290.txt │ │ ├── omim-620094.txt │ │ ├── omim-620102.txt │ │ ├── omim-620103.txt │ │ ├── omim-620104.txt │ │ └── omim-620107.txt │ ├── io │ ├── __init__.py │ ├── exporter.py │ ├── html_exporter.py │ └── markdown_exporter.py │ ├── templates │ ├── __init__.py │ ├── all.yaml │ ├── biological_process.py │ ├── biological_process.yaml │ ├── core.py │ ├── core.yaml │ ├── drug.py │ ├── drug.yaml │ ├── environmental_sample.py │ ├── environmental_sample.yaml │ ├── gocam.py │ ├── gocam.yaml │ ├── mendelian_disease.py │ ├── mendelian_disease.yaml │ ├── metabolic_process.py │ ├── metabolic_process.yaml │ ├── metagenome_study.py │ ├── metagenome_study.yaml │ ├── ontology_class.py │ ├── ontology_class.yaml │ ├── reaction.py │ ├── reaction.yaml │ ├── recipe.py │ ├── recipe.yaml │ ├── treatment.py │ └── treatment.yaml │ └── webapp │ ├── __init__.py │ ├── html │ ├── form.html │ └── results.html │ └── main.py ├── tests ├── __init__.py ├── input │ ├── cases │ │ ├── drug-DB00316-moa.txt │ │ ├── environment-jgi1.txt │ │ ├── environment-jgi2.txt │ │ ├── environment-jgi2.yaml │ │ ├── environmental-sample-hyporheic.txt │ │ ├── gocam-27929086.txt │ │ ├── gocam-33246504.txt │ │ ├── gocam-betacat.txt │ │ ├── mendelian-disease-marfan.txt │ │ ├── mendelian-disease-sly.txt │ │ ├── reaction-20657015.txt │ │ ├── reaction-21290071.txt │ │ ├── recipe-1.txt │ │ ├── recipe-2.txt │ │ ├── recipe-3.txt │ │ └── treatment-marfan.txt │ ├── eds-output.pickle │ ├── eds-output.yaml │ ├── example-raw-output.txt │ ├── instances │ │ ├── biological-process-cysteine-biosynthesis.yaml │ │ ├── drug-mechanisms-001.yaml │ │ ├── ontology-class-ncit-001.yaml │ │ └── reactions-001.yaml │ ├── inter-organism.yaml │ ├── prompts │ │ └── nedema-prompt.yaml │ └── training │ │ └── training-mendelian-disease-001.yaml ├── output │ ├── README.md │ ├── drug-DB00316-moa.yaml │ ├── eds-output.html │ ├── eds-output.md │ ├── environmental-sample-hyporheic.yaml │ ├── eval-go-examples.yaml │ ├── eval-go-predictions.yaml │ ├── generalized-drug-mechanisms-001.yaml │ ├── generalized-reactions-001.yaml │ ├── gocam-27929086.yaml │ ├── gocam-33246504.yaml │ ├── gocam-betacat.yaml │ ├── mendelian-disease-marfan.yaml │ ├── mendelian-disease-sly.yaml │ ├── reaction-20657015.yaml │ ├── reaction-21290071.yaml │ └── treatment-marfan.yaml ├── test_clients │ ├── __init__.py │ └── test_openai_client.py ├── test_evaluation │ ├── __init__.py │ ├── test_eval_drugmechdb.py │ ├── test_eval_go.py │ └── test_eval_hpoa.py ├── test_exporters │ ├── __init__.py │ ├── test_html_exporter.py │ └── test_markdown_exporter.py └── test_knowledge_extractor │ ├── __init__.py │ ├── test_cases.py │ ├── test_generalizations.py │ └── test_knowledge_extractor.py └── tox.ini /.cruft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cmungall/semantic-llama/HEAD/.cruft.json 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