├── .gitignore ├── LICENSE ├── README.md ├── app ├── __init__.py ├── result_parser.py ├── static │ ├── css │ │ ├── default.css │ │ ├── documentation.css │ │ ├── index.css │ │ ├── loader.css │ │ ├── sb-admin-2.min.css │ │ └── tooltip.css │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── images │ │ ├── favicon.ico │ │ └── logo_new.png │ └── js │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ ├── jquery.easing.min.js │ │ ├── jquery.min.js │ │ ├── jquery.min.map │ │ ├── main.js │ │ └── sb-admin-2.min.js ├── temp │ ├── dummy1_20211129.json │ └── dummy2_20111129.json └── templates │ ├── api_content.html │ ├── documentation.html │ ├── footer.html │ ├── header.html │ ├── index.html │ ├── local_content.html │ ├── navbar.html │ └── result_text.html ├── bern2.png ├── bern2 ├── __init__.py ├── bern2.py ├── convert.py └── normalizer.py ├── multi_ner ├── __init__.py ├── convert.py ├── main.py ├── modeling.py ├── ner_server.py ├── ops.py └── training │ ├── README.md │ ├── modeling.py │ ├── run_eval.py │ ├── run_ner.py │ └── utils_ner.py ├── normalizers ├── __init__.py ├── cellline_normalizer.py ├── celltype_normalizer.py ├── chemical_normalizer.py ├── neural_normalizer.py ├── readme.md └── species_normalizer.py ├── preprocess ├── preprocess_cellontology.py └── preprocess_cellosaurus.py ├── requirements.txt ├── scripts ├── run_bern2.sh ├── run_bern2_cpu.sh ├── run_bern2_windows.sh └── stop_bern2.sh └── server.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BERN2/HEAD/.gitignore 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