├── .gitignore ├── .python-version ├── CHANGELOG.md ├── LICENSE ├── README.md ├── analyses └── threshold.ipynb ├── database ├── README.md ├── annotations │ ├── README.md │ ├── demner-fushman-test-labels.json │ ├── demner-fushman-train-labels.json │ ├── eu-annot.json │ ├── fda-pediatric-special-populations-annot.json │ ├── jp-annot.json │ └── uk-annot.json ├── database_scripts │ ├── mysql.sh │ ├── postgres.sh │ └── sqlite.sh ├── schema │ ├── mysql.sql │ ├── postgres.sql │ └── sqlite.sql ├── summarize.sql └── test.sql ├── docs ├── README.md └── schema.png ├── flake.lock ├── flake.nix ├── pyproject.toml ├── snakemake ├── eu │ ├── download │ │ └── Snakefile │ └── parse │ │ └── Snakefile ├── jp │ ├── download │ │ └── Snakefile │ └── parse │ │ └── Snakefile ├── onsides │ ├── evaluate │ │ ├── Snakefile │ │ ├── format_labels.sql │ │ ├── meddra_jp_to_eng.sql │ │ └── meddra_vocabs.sql │ └── export │ │ ├── Snakefile │ │ ├── eu_mapping.sql │ │ ├── filter_deficient.sql │ │ ├── final_vocabulary_tables.sql │ │ ├── high_confidence.sql │ │ ├── japan_mapping.sql │ │ ├── rxnav-path-table.html │ │ ├── rxnorm_match_vocabulary.sql │ │ ├── threshold.sql │ │ ├── uk_mapping.sql │ │ └── us_mapping.sql ├── uk │ ├── download │ │ └── Snakefile │ └── parse │ │ └── Snakefile └── us │ ├── download │ └── Snakefile │ └── parse │ └── Snakefile ├── src └── onsides │ ├── __init__.py │ ├── cli.py │ ├── clinicalbert.py │ ├── db.py │ ├── download_utils.py │ ├── export_schema.py │ ├── parse_utils.py │ ├── predict.py │ ├── rxnorm.py │ ├── rxnorm_ingredients.py │ ├── stringsearch.py │ ├── test_stringsearch.py │ └── types.py ├── train └── script.sh └── uv.lock /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tatonetti-lab/onsides/HEAD/.gitignore -------------------------------------------------------------------------------- /.python-version: 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