Oumaima El Khettari, Solen Quiniou, Samuel Chaffron
{"title":"Building a Corpus for Biomedical Relation Extraction of Species Mentions","authors":"Oumaima El Khettari, Solen Quiniou, Samuel Chaffron","doi":"10.48550/arXiv.2306.08403","DOIUrl":null,"url":null,"abstract":"We present a manually annotated new corpus, Species-Species Interaction (SSI), for extracting meaningful binary relations between species, in biomedical texts, at sentence level, with a focus on the gut microbiota. The corpus leverages PubTator to annotate species in full-text articles after evaluating different NER species taggers. Our first results are promising for extracting relations between species using BERT and its biomedical variants.","PeriodicalId":200974,"journal":{"name":"Workshop on Biomedical Natural Language Processing","volume":"1 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Workshop on Biomedical Natural Language Processing","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.48550/arXiv.2306.08403","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
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Abstract
We present a manually annotated new corpus, Species-Species Interaction (SSI), for extracting meaningful binary relations between species, in biomedical texts, at sentence level, with a focus on the gut microbiota. The corpus leverages PubTator to annotate species in full-text articles after evaluating different NER species taggers. Our first results are promising for extracting relations between species using BERT and its biomedical variants.
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