├── .gitignore ├── .travis.yml ├── LICENSE-BSD.md ├── LICENSE-CC0.md ├── README.md ├── config_files ├── CONFIG.md ├── README.md ├── pubtator_central_config.json ├── pubtator_config.json └── tests_config.json ├── data ├── .gitattributes ├── example │ ├── 1-sample-annotations.txt │ ├── 2-sample-docs.xml │ ├── 3-sample-tags.tsv │ ├── 4-hetnet-tags.tsv │ ├── 5-sample-pmids-to-pmcids.tsv │ ├── 6-sample-full-text.xml │ ├── 7-sample-full-text-tags.tsv │ ├── 8-hetnet-full-text-tags.tsv │ ├── README.md │ └── ncbi_pmid_to_pmcid_map.tsv.xz └── temp │ ├── batch_0.xml │ ├── batch_1.xml │ └── batch_log.tsv ├── download └── bioconcepts2pubtator_offsets.gz.log ├── execute.py ├── mapper ├── drugbank_mapper.tsv └── map_to_drugbank.py ├── requirements.txt ├── scripts ├── __init__.py ├── download_full_text.py ├── extract_tags.py ├── hetnet_id_extractor.py ├── map_ids.py ├── pubtator_to_xml.py └── utilities.py └── tests.sh /.gitignore: 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