{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,15]],"date-time":"2026-08-15T09:53:00Z","timestamp":1786787580145,"version":"build-2736575974"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,8,8]],"date-time":"2020-08-08T00:00:00Z","timestamp":1596844800000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health Intramural Research Program, National Library of Medicine"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>To obtain key information for personalized medicine and cancer research, clinicians and researchers in the biomedical field are in great need of searching genomic variant information from the biomedical literature now than ever before. Due to the various written forms of genomic variants, however, it is difficult to locate the right information from the literature when using a general literature search system. To address the difficulty of locating genomic variant information from the literature, researchers have suggested various solutions based on automated literature-mining techniques. There is, however, no study for summarizing and comparing existing tools for genomic variant literature mining in terms of how to search easily for information in the literature on genomic variants.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we systematically compared currently available genomic variant recognition and normalization tools as well as the literature search engines that adopted these literature-mining techniques. First, we explain the problems that are caused by the use of non-standard formats of genomic variants in the PubMed literature by considering examples from the literature and show the prevalence of the problem. Second, we review literature-mining tools that address the problem by recognizing and normalizing the various forms of genomic variants in the literature and systematically compare them. Third, we present and compare existing literature search engines that are designed for a genomic variant search by using the literature-mining techniques. We expect this work to be helpful for researchers who seek information about genomic variants from the literature, developers who integrate genomic variant information from the literature and beyond.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbaa142","type":"journal-article","created":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T19:09:52Z","timestamp":1591729792000},"source":"Crossref","is-referenced-by-count":24,"title":["Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature"],"prefix":"10.1093","volume":"22","author":[{"given":"Kyubum","family":"Lee","sequence":"first","affiliation":[{"name":"National Center for Biotechnology Information"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih-Hsuan","family":"Wei","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,8,7]]},"reference":[{"key":"2021052110184168000_ref1","volume":"12"},{"issue":"7573","key":"2021052110184168000_ref2","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/nature15816","article-title":"Building the foundation for genomics in precision medicine","volume":"526","author":"Aronson","year":"2015","journal-title":"Nature"},{"issue":"268","key":"2021052110184168000_ref3","doi-asserted-by":"crossref","first-page":"eg3","DOI":"10.1126\/scisignal.2004149","article-title":"Focus issue: from genomic mutations to oncogenic pathways","volume":"6","author":"Gough","year":"2013","journal-title":"Sci Signal"},{"issue":"7378","key":"2021052110184168000_ref4","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature10673","article-title":"Cancer immunotherapy comes of age","volume":"480","author":"Mellman","year":"2011","journal-title":"Nature"},{"issue":"10","key":"2021052110184168000_ref5","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/nbt.4267","article-title":"How user intelligence is improving PubMed","volume":"36","author":"Fiorini","year":"2018","journal-title":"Nat Biotechnol"},{"issue":"D1","key":"2021052110184168000_ref6","doi-asserted-by":"crossref","first-page":"D777","DOI":"10.1093\/nar\/gkw1121","article-title":"COSMIC: somatic cancer genetics at high-resolution","volume":"45","author":"Forbes","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2021052110184168000_ref7","doi-asserted-by":"crossref","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","article-title":"The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)","volume":"45","author":"MacArthur","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"2021052110184168000_ref8","doi-asserted-by":"crossref","first-page":"i41","DOI":"10.1093\/bioinformatics\/btm229","article-title":"Manual curation is not sufficient for annotation of genomic databases","volume":"23","author":"Baumgartner","year":"2007","journal-title":"Bioinformatics"},{"issue":"21","key":"2021052110184168000_ref9","doi-asserted-by":"crossref","first-page":"3454","DOI":"10.1093\/bioinformatics\/btx439","article-title":"On expert curation and scalability: UniProtKB\/Swiss-Prot as a case study","volume":"33","author":"Poux","year":"2017","journal-title":"Bioinformatics"},{"key":"2021052110184168000_ref10","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bau039","article-title":"BioCreative-IV virtual issue","volume":"2014","author":"Arighi","year":"2014","journal-title":"Database"},{"issue":"8","key":"2021052110184168000_ref11","doi-asserted-by":"crossref","first-page":"e1006390","DOI":"10.1371\/journal.pcbi.1006390","article-title":"Scaling up data curation using deep learning: an application to literature triage in genomic variation resources","volume":"14","author":"Lee","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"2021052110184168000_ref12","doi-asserted-by":"crossref","first-page":"e1005017","DOI":"10.1371\/journal.pcbi.1005017","article-title":"Text mining genotype-phenotype relationships from biomedical literature for database curation and precision medicine","volume":"12","author":"Singhal","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"2021052110184168000_ref13","first-page":"366856","article-title":"A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants","author":"Wagner","year":"2018","journal-title":"bioRxiv"},{"issue":"6","key":"2021052110184168000_ref14","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1002\/humu.22981","article-title":"HGVS recommendations for the description of sequence variants: 2016 update","volume":"37","author":"den Dunnen","year":"2016","journal-title":"Hum Mutat"},{"issue":"1","key":"2021052110184168000_ref15","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2021052110184168000_ref16","article-title":"Helping us help you, and millions: how authors can help advance data-driven discovery","author":"Leaman","year":"2020","journal-title":"PLoS Biol"},{"issue":"11","key":"2021052110184168000_ref17","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1038\/ng.3716","article-title":"Genome variation for non-geneticists","volume":"48","year":"2016","journal-title":"Nat Genet"},{"issue":"3","key":"2021052110184168000_ref18","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1002\/humu.10262","article-title":"Standardizing mutation nomenclature: why bother?","volume":"22","author":"den Dunnen","year":"2003","journal-title":"Hum Mutat"},{"issue":"11","key":"2021052110184168000_ref19","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1002\/humu.21569","article-title":"Mutation nomenclature in practice: findings and recommendations from the cystic fibrosis external quality assessment scheme","volume":"32","author":"Berwouts","year":"2011","journal-title":"Hum Mutat"},{"issue":"6","key":"2021052110184168000_ref20","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1002\/humu.22978","article-title":"HGVS nomenclature in practice: an example from the United Kingdom National External Quality Assessment Scheme","volume":"37","author":"Deans","year":"2016","journal-title":"Hum Mutat"},{"issue":"6","key":"2021052110184168000_ref21","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1002\/humu.22975","article-title":"What's in a name? A coordinated approach toward the correct use of a uniform nomenclature to improve patient reports and databases","volume":"37","author":"Tack","year":"2016","journal-title":"Hum Mutat"},{"issue":"18","key":"2021052110184168000_ref22","doi-asserted-by":"crossref","first-page":"3533","DOI":"10.1093\/bioinformatics\/btz070","article-title":"PMC text mining subset in BioC: about three million full-text articles and growing","volume":"35","author":"Comeau","year":"2019","journal-title":"Bioinformatics"},{"issue":"6","key":"2021052110184168000_ref23","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1016\/j.gpb.2012.06.006","article-title":"The curation of genetic variants: difficulties and possible solutions","volume":"10","author":"Pandey","year":"2012","journal-title":"Genomics Proteomics Bioinformatics"},{"issue":"1","key":"2021052110184168000_ref24","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1093\/bioinformatics\/btx541","article-title":"tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine","volume":"34","author":"Wei","year":"2017","journal-title":"Bioinformatics"},{"issue":"18","key":"2021052110184168000_ref25","doi-asserted-by":"crossref","first-page":"2883","DOI":"10.1093\/bioinformatics\/btw234","article-title":"SETH detects and normalizes genetic variants in text","volume":"32","author":"Thomas","year":"2016","journal-title":"Bioinformatics"},{"issue":"14","key":"2021052110184168000_ref26","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"},{"issue":"Suppl 4","key":"2021052110184168000_ref27","doi-asserted-by":"crossref","first-page":"S24","DOI":"10.1186\/1471-2164-11-S4-S24","article-title":"Algorithms and semantic infrastructure for mutation impact extraction and grounding","volume":"11","author":"Laurila","year":"2010","journal-title":"BMC Genomics"},{"issue":"4","key":"2021052110184168000_ref28","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2164-13-S4-S10","article-title":"Automated extraction and semantic analysis of mutation impacts from the biomedical literature","volume":"13","author":"Naderi","year":"2012","journal-title":"BMC Genomics"},{"issue":"3","key":"2021052110184168000_ref29","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1093\/bioinformatics\/btq667","article-title":"Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature","volume":"27","author":"Doughty","year":"2010","journal-title":"Bioinformatics"},{"key":"2021052110184168000_ref30","doi-asserted-by":"crossref","first-page":"bau094","DOI":"10.1093\/database\/bau094","article-title":"Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing","volume":"2014","author":"Burger","year":"2014","journal-title":"Database (Oxford)"},{"issue":"8","key":"2021052110184168000_ref31","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2105-12-S8-S5","article-title":"Cross-species gene normalization by species inference","volume":"12","author":"Wei","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"19","key":"2021052110184168000_ref32","doi-asserted-by":"crossref","first-page":"2769","DOI":"10.1093\/bioinformatics\/btr455","article-title":"The GNAT library for local and remote gene mention normalization","volume":"27","author":"Hakenberg","year":"2011","journal-title":"Bioinformatics"},{"issue":"11","key":"2021052110184168000_ref33","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1093\/bioinformatics\/btt156","article-title":"tmVar: a text mining approach for extracting sequence variants in biomedical literature","volume":"29","author":"Wei","year":"2013","journal-title":"Bioinformatics"},{"key":"2021052110184168000_ref34","article-title":"GNormPlus: an integrative approach for tagging genes, gene families, and protein domains","volume":"918710","author":"Wei","year":"2015","journal-title":"Biomed Res Int"},{"issue":"W1","key":"2021052110184168000_ref35","doi-asserted-by":"crossref","first-page":"W587","DOI":"10.1093\/nar\/gkz389","article-title":"PubTator central: automated concept annotation for biomedical full text articles","volume":"47","author":"Wei","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2021052110184168000_ref36","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/s41436-019-0643-6","article-title":"AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature","volume":"22","author":"Birgmeier","year":"2019","journal-title":"Genet Med"},{"key":"2021052110184168000_ref37","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baw043","article-title":"BRONCO: biomedical entity relation ONcology COrpus for extracting gene-variant-disease-drug relations","volume":"2016","author":"Lee","year":"2016","journal-title":"Database"},{"issue":"4","key":"2021052110184168000_ref38","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-12-S4-S4","article-title":"Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers","volume":"12","author":"Thomas","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2021052110184168000_ref39","article-title":"Mutation extraction tools can be combined for robust recognition of genetic variants in the literature","volume":"3","author":"Yepes","year":"2014","journal-title":"F1000Research"},{"key":"2021052110184168000_ref40","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bat019","article-title":"Annotating the biomedical literature for the human variome","volume":"2013","author":"Verspoor","year":"2013","journal-title":"Database"},{"issue":"1","key":"2021052110184168000_ref41","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1093\/nar\/gkh162","article-title":"Automatic extraction of mutations from Medline and cross-validation with OMIM","volume":"32","author":"Rebholz-Schuhmann","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2021052110184168000_ref42","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/bioinformatics\/btg449","article-title":"Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors","volume":"20","author":"Horn","year":"2004","journal-title":"Bioinformatics"},{"issue":"2","key":"2021052110184168000_ref43","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1371\/journal.pcbi.0030016","article-title":"Automatic extraction of protein point mutations using a Graph Bigram association","volume":"3","author":"Lee","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"2021052110184168000_ref44","first-page":"89","article-title":"UniProtKB\/Swiss-Prot","volume":"406","author":"Boutet","year":"2007","journal-title":"Methods Mol Biol (Clifton, NJ)"},{"issue":"6","key":"2021052110184168000_ref45","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1142\/S021972000700320X","article-title":"Retrieving mutation-specific information for human proteins in UniProt\/Swiss-Prot knowledgebase","volume":"5","author":"Yip","year":"2007","journal-title":"J Bioinform Comput Biol"},{"issue":"4","key":"2021052110184168000_ref46","doi-asserted-by":"crossref","first-page":"e0152725","DOI":"10.1371\/journal.pone.0152725","article-title":"DiMeX: a text mining system for mutation-disease association extraction","volume":"11","author":"Mahmood","year":"2016","journal-title":"PLoS One"},{"issue":"17","key":"2021052110184168000_ref47","doi-asserted-by":"crossref","first-page":"3249","DOI":"10.1093\/bioinformatics\/bth350","article-title":"An entity tagger for recognizing acquired genomic variations in cancer literature","volume":"20","author":"McDonald","year":"2004","journal-title":"Bioinformatics"},{"issue":"6","key":"2021052110184168000_ref48","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1142\/S021972000700317X","article-title":"Application of automatic mutation-gene pair extraction to diseases","volume":"5","author":"Erdogmus","year":"2007","journal-title":"J Bioinform Comput Biol"},{"issue":"1","key":"2021052110184168000_ref49","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/s10791-008-9074-8","article-title":"Evaluation of query expansion using MeSH in PubMed","volume":"12","author":"Lu","year":"2009","journal-title":"Inf Retr Boston"},{"issue":"W1","key":"2021052110184168000_ref50","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":"2021052110184168000_ref51","article-title":"variant2literature: full text literature search for genetic variants","author":"Lin","year":"2019","journal-title":"bioRxiv"},{"issue":"1","key":"2021052110184168000_ref52","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1186\/s12859-019-2958-3","article-title":"VIST - a variant-information search tool for precision oncology","volume":"20","author":"\u0160eva","year":"2019","journal-title":"BMC Bioinformatics"},{"issue":"W1","key":"2021052110184168000_ref53","doi-asserted-by":"crossref","first-page":"W518","DOI":"10.1093\/nar\/gkt441","article-title":"PubTator: a web-based text mining tool for assisting biocuration","volume":"41","author":"Wei","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"2021052110184168000_ref54","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1056\/NEJMsr1611785","article-title":"Trial reporting in ClinicalTrials.gov\u2014the final rule","volume":"375","author":"Zarin","year":"2016","journal-title":"N Engl J Med"},{"issue":"10","key":"2021052110184168000_ref55","doi-asserted-by":"crossref","first-page":"e0164680","DOI":"10.1371\/journal.pone.0164680","article-title":"BEST: next-generation biomedical entity search tool for knowledge discovery from biomedical literature","volume":"11","author":"Lee","year":"2016","journal-title":"PLoS One"},{"issue":"W1","key":"2021052110184168000_ref56","doi-asserted-by":"crossref","first-page":"W585","DOI":"10.1093\/nar\/gks563","article-title":"GeneView: a comprehensive semantic search engine for PubMed","volume":"40","author":"Thomas","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2021052110184168000_ref57","author":"Mastermind Genomic Search Engine"},{"issue":"1","key":"2021052110184168000_ref58","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1002\/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N","article-title":"Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion","volume":"15","author":"den Dunnen","year":"2000","journal-title":"Hum Mutat"},{"issue":"1","key":"2021052110184168000_ref59","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/s004390100505","article-title":"Nomenclature for the description of human sequence variations","volume":"109","author":"den Dunnen","year":"2001","journal-title":"Hum Genet"},{"issue":"6","key":"2021052110184168000_ref60","doi-asserted-by":"crossref","first-page":"e3000716","DOI":"10.1371\/journal.pbio.3000716","article-title":"Ten tips for a text-mining-ready article: how to improve automated discoverability and interpretability","volume":"18","author":"Leaman","year":"2020","journal-title":"PLoS Biol"},{"issue":"8","key":"2021052110184168000_ref61","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1002\/humu.23830","article-title":"Efficient variant data preparation for human mutation manuscripts: variants and phenotypes","volume":"40","author":"den Dunnen","year":"2019","journal-title":"Hum Mutat"},{"issue":"D1","key":"2021052110184168000_ref62","doi-asserted-by":"crossref","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","article-title":"ClinVar: improving access to variant interpretations and supporting evidence","volume":"46","author":"Landrum","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2021052110184168000_ref63","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1002\/humu.21438","article-title":"LOVD v. 2.0: the next generation in gene variant databases","volume":"32","author":"Fokkema","year":"2011","journal-title":"Hum Mutat"},{"issue":"1","key":"2021052110184168000_ref64","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1002\/humu.23348","article-title":"VariantValidator: accurate validation, mapping, and formatting of sequence variation descriptions","volume":"39","author":"Freeman","year":"2018","journal-title":"Hum Mutat"},{"issue":"12","key":"2021052110184168000_ref65","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1002\/humu.23615","article-title":"hgvs: a Python package for manipulating sequence variants using HGVS nomenclature: 2018 update","volume":"39","author":"Wang","year":"2018","journal-title":"Hum Mutat"},{"issue":"1","key":"2021052110184168000_ref66","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1002\/humu.20654","article-title":"Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker","volume":"29","author":"Wildeman","year":"2008","journal-title":"Hum Mutat"},{"key":"2021052110184168000_ref67","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.bcmd.2018.05.001","article-title":"Biomarker signatures of sickle cell disease severity","volume":"72","author":"Du","year":"2018","journal-title":"Blood Cells Mol Dis"},{"key":"2021052110184168000_ref68","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btaa111","article-title":"DL4papers: a deep learning approach for the automatic interpretation of scientific articles","volume":"36","author":"Bugnon","year":"2020","journal-title":"Bioinformatics"},{"issue":"1","key":"2021052110184168000_ref69","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1186\/s12859-019-3321-4","article-title":"Biomedical named entity recognition using deep neural networks with contextual information","volume":"20","author":"Cho","year":"2019","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"2021052110184168000_ref70","doi-asserted-by":"crossref","first-page":"e0216046","DOI":"10.1371\/journal.pone.0216046","article-title":"Deep learning for named entity recognition on Chinese electronic medical records: combining deep transfer learning with multitask bi-directional LSTM RNN","volume":"14","author":"Dong","year":"2019","journal-title":"PLOS ONE"},{"key":"2021052110184168000_ref71","article-title":"Transfer learning in biomedical natural language processing: an evaluation of BERT and ELMo on ten benchmarking datasets","author":"Peng","year":"2019","journal-title":"arXiv Preprint"},{"issue":"6","key":"2021052110184168000_ref72","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1142\/S0219720007003119","article-title":"A workflow for mutation extraction and structure annotation","volume":"5","author":"Kanagasabai","year":"2007","journal-title":"J Bioinform Comput Biol"},{"key":"2021052110184168000_ref73","article-title":"variant2literature: full text literature search for genetic variants","author":"Lin","year":"2019","journal-title":"bioRxiv"},{"issue":"1","key":"2021052110184168000_ref74","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/1471-2105-9-84","article-title":"OSIRISv1. 2: a named entity recognition system for sequence variants of genes in biomedical literature","volume":"9","author":"Furlong","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"2021052110184168000_ref75","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-10-S8-S4","article-title":"Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb","volume":"10","author":"Nagel","year":"2009","journal-title":"BMC Bioinformatics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/3\/bbaa142\/37966186\/bbaa142.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/22\/3\/bbaa142\/37966186\/bbaa142.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,21]],"date-time":"2021-05-21T10:20:25Z","timestamp":1621592425000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaa142\/5882186"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,7]]},"references-count":75,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,5,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaa142","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,5]]},"published":{"date-parts":[[2020,8,7]]},"article-number":"bbaa142"}}