{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T16:17:57Z","timestamp":1759940277678},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2055,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Increasing rates of publication and DNA sequencing make the problem of finding relevant articles for a particular gene or genomic region more challenging than ever. Existing text-mining approaches focus on finding gene names or identifiers in English text. These are often not unique and do not identify the exact genomic location of a study.<\/jats:p>\n               <jats:p>Results: Here, we report the results of a novel text-mining approach that extracts DNA sequences from biomedical articles and automatically maps them to genomic databases. We find that \u223c20% of open access articles in PubMed central (PMC) have extractable DNA sequences that can be accurately mapped to the correct gene (91%) and genome (96%). We illustrate the utility of data extracted by text2genome from more than 150 000 PMC articles for the interpretation of ChIP-seq data and the design of quantitative reverse transcriptase (RT)-PCR experiments.<\/jats:p>\n               <jats:p>Conclusion: Our approach links articles to genes and organisms without relying on gene names or identifiers. It also produces genome annotation tracks of the biomedical literature, thereby allowing researchers to use the power of modern genome browsers to access and analyze publications in the context of genomic data.<\/jats:p>\n               <jats:p>Availability and implementation: Source code is available under a BSD license from http:\/\/sourceforge.net\/projects\/text2genome\/ and results can be browsed and downloaded at http:\/\/text2genome.org.<\/jats:p>\n               <jats:p>Contact: \u00a0maximilianh@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr043","type":"journal-article","created":{"date-parts":[[2011,2,17]],"date-time":"2011-02-17T01:15:09Z","timestamp":1297905309000},"page":"980-986","source":"Crossref","is-referenced-by-count":22,"title":["Annotating genes and genomes with DNA sequences extracted from biomedical articles"],"prefix":"10.1093","volume":"27","author":[{"given":"Maximilian","family":"Haeussler","sequence":"first","affiliation":[{"name":"Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Gerner","sequence":"additional","affiliation":[{"name":"Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Casey M.","family":"Bergman","sequence":"additional","affiliation":[{"name":"Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,2,16]]},"reference":[{"key":"2023012512171309000_B1","doi-asserted-by":"crossref","first-page":"R31","DOI":"10.1186\/gb-2008-9-2-r31","article-title":"Text-mining assisted regulatory annotation","volume":"9","author":"Aerts","year":"2008","journal-title":"Genome Biol."},{"key":"2023012512171309000_B2","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1186\/1471-2105-7-260","article-title":"On the persistence of supplementary resources in biomedical publications","volume":"7","author":"Anderson","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012512171309000_B3","doi-asserted-by":"crossref","first-page":"D46","DOI":"10.1093\/nar\/gkp1024","article-title":"GenBank","volume":"38","author":"Benson","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512171309000_B4","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"issue":"Suppl. 1","key":"2023012512171309000_B5","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1186\/1471-2105-6-S1-S12","article-title":"Data preparation and interannotator agreement: BioCreAtIvE task 1B","volume":"6","author":"Colosimo","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012512171309000_B6","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-2-7","article-title":"The distributed annotation system","volume":"2","author":"Dowell","year":"2001","journal-title":"BMC Bioinformatics"},{"key":"2023012512171309000_B7","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1093\/nar\/gkg094","article-title":"The FlyBase database of the Drosophila genome projects and community literature","volume":"31","author":"The FlyBase Consortium","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012512171309000_B8","doi-asserted-by":"crossref","first-page":"3740","DOI":"10.1093\/hmg\/ddn271","article-title":"Identification of Arx transcriptional targets in the developing basal forebrain","volume":"17","author":"Fulp","year":"2008","journal-title":"Hum. 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