{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T13:53:11Z","timestamp":1769608391662,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T00:00:00Z","timestamp":1659052800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institutes of Health Intramural Research Program"},{"DOI":"10.13039\/100000092","name":"National Library of Medicine","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"NHGRI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Clinical Genome Resource","award":["U24 HG009649"],"award-info":[{"award-number":["U24 HG009649"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision.<\/jats:p><\/jats:sec><jats:sec><jats:title>Result<\/jats:title><jats:p>We propose tmVar 3.0: an improved variant recognition and normalization system. Compared to its predecessors, tmVar 3.0 recognizes a wider spectrum of variant-related entities (e.g. allele and copy number variants), and groups together different variant mentions belonging to the same genomic sequence position in an article for improved accuracy. Moreover, tmVar 3.0 provides advanced variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar 3.0 exhibits state-of-the-art performance with over 90% in F-measure for variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar 3.0 as well as annotations for the entire PubMed and PMC datasets are freely available for download.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/github.com\/ncbi\/tmVar3<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac537","type":"journal-article","created":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T15:09:29Z","timestamp":1659107369000},"page":"4449-4451","source":"Crossref","is-referenced-by-count":22,"title":["tmVar 3.0: an improved variant concept recognition and normalization tool"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5094-7321","authenticated-orcid":false,"given":"Chih-Hsuan","family":"Wei","sequence":"first","affiliation":[{"name":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , Bethesda, MD 20894, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2706-9054","authenticated-orcid":false,"given":"Alexis","family":"Allot","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , Bethesda, MD 20894, USA"}]},{"given":"Kevin","family":"Riehle","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"given":"Aleksandar","family":"Milosavljevic","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9998-916X","authenticated-orcid":false,"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , Bethesda, MD 20894, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,7,29]]},"reference":[{"key":"2023041408375119400_","doi-asserted-by":"crossref","first-page":"W530","DOI":"10.1093\/nar\/gky355","article-title":"LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC","volume":"46","author":"Allot","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023041408375119400_","doi-asserted-by":"crossref","first-page":"2567","DOI":"10.1093\/bioinformatics\/btl421","article-title":"OSIRIS: a tool for retrieving literature about sequence variants","volume":"22","author":"Bonis","year":"2006","journal-title":"Bioinformatics"},{"key":"2023041408375119400_","doi-asserted-by":"crossref","first-page":"1862","DOI":"10.1093\/bioinformatics\/btm235","article-title":"MutationFinder: a high-performance system for extracting point mutation mentions from text","volume":"23","author":"Caporaso","year":"2007","journal-title":"Bioinformatics"},{"key":"2023041408375119400_","doi-asserted-by":"crossref","first-page":"1852","DOI":"10.1093\/bioinformatics\/btx083","article-title":"nala: text mining natural language mutation mentions","volume":"33","author":"Cejuela","year":"2017","journal-title":"Bioinformatics"},{"key":"2023041408375119400_","first-page":"598","article-title":"DeepVar: an end-to-end deep learning approach for genomic variant recognition in biomedical literature","volume":"34","author":"Cheng","year":"2020","journal-title":"Proc. AAAI Conf. Artif. Intell"},{"key":"2023041408375119400_","doi-asserted-by":"crossref","first-page":"bbaa142","DOI":"10.1093\/bib\/bbaa142","article-title":"Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature","volume":"22","author":"Lee","year":"2021","journal-title":"Brief. Bioinform"},{"key":"2023041408375119400_","first-page":"67","article-title":"LitGen: Genetic literature recommendation guided by human explanations","volume":"25","author":"Nie","year":"2019","journal-title":"Pac. Symp. Biocomput"},{"key":"2023041408375119400_","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1002\/humu.23637","article-title":"ClinGen allele registry links information about genetic variants","volume":"39","author":"Pawliczek","year":"2018","journal-title":"Hum. 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