{"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/a-silver-standard-corpus-of-human-phenotype","title":"A Silver Standard Corpus of Human Phenotype-Gene Relations","arxiv_id":"1903.10728","date":"2019-03-26","proceeding":"NAACL 2019 6","authors":["Diana Sousa","Andre Lamurias","Francisco M. Couto"],"abstract":"Human phenotype-gene relations are fundamental to fully understand the origin of some phenotypic abnormalities and their associated diseases. Biomedical literature is the most comprehensive source of these relations, however, we need Relation Extraction tools to automatically recognize them. Most of these tools require an annotated corpus and to the best of our knowledge, there is no corpus available annotated with human phenotype-gene relations. This paper presents the Phenotype-Gene Relations (PGR) corpus, a silver standard corpus of human phenotype and gene annotations and their relations. The corpus consists of 1712 abstracts, 5676 human phenotype annotations, 13835 gene annotations, and 4283 relations. We generated this corpus using Named-Entity Recognition tools, whose results were partially evaluated by eight curators, obtaining a precision of 87.01%. By using the corpus we were able to obtain promising results with two state-of-the-art deep learning tools, namely 78.05% of precision. The PGR corpus was made publicly available to the research community.","url_abs":"https://arxiv.org/abs/1903.10728v2","url_pdf":"https://arxiv.org/pdf/1903.10728v2.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":"a-silver-standard-corpus-of-human-phenotype","repo_url":"https://github.com/lasigeBioTM/PGR","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"jax","reach":null}],"tasks":[{"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":"relation-extraction","task_name":"Relation Extraction"},{"task_slug":"named-entity-recognition","task_name":"named-entity-recognition"}],"methods":[],"datasets_introduced":[{"slug":"pgr","name":"PGR","full_name":"Phenotype-Gene Relations"}],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/1903.10728","atlas_url":"https://app.syntology.ai/?focus=1903.10728","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}