├── .flake8 ├── .github ├── CODEOWNERS └── workflows │ └── run-tests.yml ├── .gitignore ├── .pre-commit-config.yaml ├── README.md ├── config.ini ├── dataset ├── coronavirus │ ├── Genome identity.csv │ └── Host proteins (potential drug targets).csv ├── semmed │ ├── Object_CORD_NER.csv │ ├── README.md │ └── Subject_CORD_NER.csv └── uniprot │ └── uniprot-reviewed_yes+AND+proteome.tsv ├── images ├── query_1.png ├── query_2.png └── query_3.png ├── loader.py ├── loader ├── __init__.py ├── coronavirus │ ├── __init__.py │ └── coronavirus_loader.py ├── dgidb │ ├── __init__.py │ └── dgidb_loader.py ├── disgenet │ ├── __init__.py │ └── disgenet_loader.py ├── hpa │ ├── __init__.py │ └── hpa_loader.py ├── reactome │ ├── __init__.py │ └── reactome_loader.py ├── semmed │ ├── __init__.py │ ├── fetch.py │ ├── load.py │ ├── mapper.py │ ├── parse.py │ └── pipeline.py ├── tissuenet │ ├── __init__.py │ ├── mapper.py │ └── tissuenet_loader.py ├── uniprot │ ├── __init__.py │ └── uniprot_loader.py └── util.py ├── pyproject.toml ├── requirements.txt ├── requirements_dev.txt ├── requirements_test.txt ├── schema ├── __init__.py ├── initialise.py └── schema.tql └── tests ├── conftest.py └── loader └── semmed └── test_semmed_migrator.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/typedb-osi/typedb-bio/HEAD/.flake8 -------------------------------------------------------------------------------- /.github/CODEOWNERS: -------------------------------------------------------------------------------- 1 | * @benjaminasmall @james-whiteside 2 | -------------------------------------------------------------------------------- /.github/workflows/run-tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/typedb-osi/typedb-bio/HEAD/.github/workflows/run-tests.yml -------------------------------------------------------------------------------- /.gitignore: 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