├── LICENSE ├── README.md ├── SECURITY.md ├── sample_notebooks ├── Interacting with the dataset.ipynb └── Sample Use Cases.ipynb ├── software-mentions-extractor ├── README.md ├── detokenizer.py ├── requirements.txt └── software-mentions-extractor.py └── software-mentions-linker-disambiguator ├── README.md ├── assign_IDs.py ├── disambiguation ├── clustering.py ├── combine_all_synonyms.py ├── generate_freq_dict.py ├── generate_string_sim_dict.py ├── generate_synonyms_keywords.py ├── generate_synonyms_scicrunch.py └── generate_synonyms_string_similarity.py ├── evaluation ├── compute_metrics_disambiguation.py ├── compute_metrics_extraction.py └── compute_metrics_linking.py ├── filter_curated_terms.py ├── initialize.py └── linking ├── bioconductor_linker.py ├── cran_linker.py ├── generate_metadata_file.py ├── github_linker.py ├── pypi_linker.py ├── scicrunch_linker.py ├── utils_common.py └── utils_linker.py /LICENSE: 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