{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/medmentions-a-large-biomedical-corpus","title":"MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts","arxiv_id":"1902.09476","date":"2019-02-25","proceeding":"AKBC 2019","authors":["Sunil Mohan","Donghui Li"],"abstract":"This paper presents the formal release of MedMentions, a new manually\nannotated resource for the recognition of biomedical concepts. What\ndistinguishes MedMentions from other annotated biomedical corpora is its size\n(over 4,000 abstracts and over 350,000 linked mentions), as well as the size of\nthe concept ontology (over 3 million concepts from UMLS 2017) and its broad\ncoverage of biomedical disciplines. In addition to the full corpus, a\nsub-corpus of MedMentions is also presented, comprising annotations for a\nsubset of UMLS 2017 targeted towards document retrieval. To encourage research\nin Biomedical Named Entity Recognition and Linking, data splits for training\nand testing are included in the release, and a baseline model and its metrics\nfor entity linking are also described.","url_abs":"http://arxiv.org/abs/1902.09476v1","url_pdf":"http://arxiv.org/pdf/1902.09476v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"medmentions-a-large-biomedical-corpus","repo_url":"https://github.com/chanzuckerberg/MedMentions","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok"}}],"tasks":[{"task_slug":"entity-linking","task_name":"Entity Linking"},{"task_slug":"named-entity-recognition-1","task_name":"Named Entity Recognition"},{"task_slug":"named-entity-recognition-ner","task_name":"Named Entity Recognition (NER)"},{"task_slug":"retrieval","task_name":"Retrieval"},{"task_slug":"named-entity-recognition","task_name":"named-entity-recognition"}],"methods":[],"datasets_introduced":[{"slug":"medmentions","name":"MedMentions","full_name":""}],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=1902.09476","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}