{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T22:50:08Z","timestamp":1761519008769},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1887,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987.<\/jats:p>\n               <jats:p>Availability: The library and web services are implemented in Java and the sources are available from http:\/\/gnat.sourceforge.net.<\/jats:p>\n               <jats:p>Contact: \u00a0jorg.hakenberg@roche.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr455","type":"journal-article","created":{"date-parts":[[2011,8,4]],"date-time":"2011-08-04T05:11:18Z","timestamp":1312434678000},"page":"2769-2771","source":"Crossref","is-referenced-by-count":53,"title":["The GNAT library for local and remote gene mention normalization"],"prefix":"10.1093","volume":"27","author":[{"given":"J\u00f6rg","family":"Hakenberg","sequence":"first","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Gerner","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maximilian","family":"Haeussler","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ill\u00e9s","family":"Solt","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Conrad","family":"Plake","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Schroeder","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graciela","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Goran","family":"Nenadic","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Casey M.","family":"Bergman","sequence":"additional","affiliation":[{"name":"1 Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA, 2Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK, 3Knowledge Management in Bioinformatics, Humboldt-Universit\u00e4t zu Berlin, 10090 Berlin, 4Computational Biology and Data Mining, Max Delbr\u00fcck Center for Molecular Medicine, 13092 Berlin, 5Biotechnology Center, Technische Universit\u00e4t Dresden, 01307 Dresden, Germany, 6Biomedical Informatics Department, Arizona State University, Phoenix, AZ 85004, USA and 7School of Computer Science, University of Manchester, Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,8,3]]},"reference":[{"key":"2023012512010961800_B1","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1093\/bioinformatics\/btq270","article-title":"TAP-k: a measure of retrieval designed for bioinformatics","volume":"26","author":"Carroll","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512010961800_B2","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1186\/1471-2105-11-85","article-title":"Linnaeus: a species name identification system for biomedical literature","volume":"11","author":"Gerner","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023012512010961800_B3","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/bioinformatics\/btr043","article-title":"Annotating genes and genomes with DNA sequences extracted from biomedical articles","volume":"27","author":"Haeussler","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512010961800_B4","doi-asserted-by":"crossref","first-page":"i126","DOI":"10.1093\/bioinformatics\/btn299","article-title":"Inter\u2013species normalization of gene mentions with GNAT","volume":"24","author":"Hakenberg","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012512010961800_B5","doi-asserted-by":"crossref","first-page":"S11","DOI":"10.1186\/1471-2105-6-S1-S11","article-title":"Overview of BioCreAtIvE task 1B: normalized gene lists","volume":"6","author":"Hirschman","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012512010961800_B6","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1093\/bioinformatics\/btr042","article-title":"GeneTUKit: a software for document-level gene normalization","volume":"27","author":"Huang","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512010961800_B7","first-page":"652","article-title":"BANNER: An executable survey of advances in biomedical named entity recognition","volume":"13","author":"Leaman","year":"2008","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012512010961800_B8","article-title":"Overview of BioCreative III Gene Normalization","volume-title":"Proceedings of the BioCreative III","author":"Lu","year":"2010"},{"key":"2023012512010961800_B9","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/gb-2008-9-s2-s3","article-title":"Overview of BioCreative II Gene Normalization","volume":"9","author":"Morgan","year":"2008","journal-title":"Genome Biol."},{"key":"2023012512010961800_B10","article-title":"Gene mention normalization in full texts using Gnatand Linnaeus","volume-title":"Proceedings of the BioCreative III","author":"Solt","year":"2010"},{"key":"2023012512010961800_B11","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/gb-2006-7-5-402","article-title":"The success (or not) of HUGO nomenclature","volume":"7","author":"Tamames","year":"2006","journal-title":"Genome Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/19\/2769\/48869884\/bioinformatics_27_19_2769.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/19\/2769\/48869884\/bioinformatics_27_19_2769.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T13:59:56Z","timestamp":1674655196000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/19\/2769\/231172"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,8,3]]},"references-count":11,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2011,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr455","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,10,1]]},"published":{"date-parts":[[2011,8,3]]}}}