{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T15:15:06Z","timestamp":1767626106425},"reference-count":10,"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":1054,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:\u2003Chemical named entity recognition is used to automatically identify mentions to chemical compounds in text and is the basis for more elaborate information extraction. However, only a small number of applications are freely available to identify such mentions. Particularly challenging and useful is the identification of International Union of Pure and Applied Chemistry (IUPAC) chemical compounds, which due to the complex morphology of IUPAC names requires more advanced techniques than that of brand names.<\/jats:p>\n               <jats:p>Results:\u2003We present CheNER, a tool for automated identification of systematic IUPAC chemical mentions. We evaluated different systems using an established literature corpus to show that CheNER has a superior performance in identifying IUPAC names specifically, and that it makes better use of computational resources.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003http:\/\/metres.udl.cat\/index.php\/9-download\/4-chener, http:\/\/chener.bioinfo.cnio.es\/<\/jats:p>\n               <jats:p>Contact:\u2003miguel.vazquez@cnio.es<\/jats:p>\n               <jats:p>Supplementary information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt639","type":"journal-article","created":{"date-parts":[[2013,11,14]],"date-time":"2013-11-14T01:41:34Z","timestamp":1384393294000},"page":"1039-1040","source":"Crossref","is-referenced-by-count":14,"title":["CheNER: chemical named entity recognizer"],"prefix":"10.1093","volume":"30","author":[{"given":"Anabel","family":"Usi\u00e9","sequence":"first","affiliation":[{"name":"1 Department of Basic Medical Science (CMB), University of Lleida & IRBLleida, 2Department of Computers an Industrial Engineering (DIEI), University of Lleida, Lleida and 3Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain"},{"name":"1 Department of Basic Medical Science (CMB), University of Lleida & IRBLleida, 2Department of Computers an Industrial Engineering (DIEI), University of Lleida, Lleida and 3Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain"}]},{"given":"Rui","family":"Alves","sequence":"additional","affiliation":[{"name":"1 Department of Basic Medical Science (CMB), University of Lleida & IRBLleida, 2Department of Computers an Industrial Engineering (DIEI), University of Lleida, Lleida and 3Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain"}]},{"given":"Francesc","family":"Solsona","sequence":"additional","affiliation":[{"name":"1 Department of Basic Medical Science (CMB), University of Lleida & IRBLleida, 2Department of Computers an Industrial Engineering (DIEI), University of Lleida, Lleida and 3Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain"}]},{"given":"Miguel","family":"V\u00e1zquez","sequence":"additional","affiliation":[{"name":"1 Department of Basic Medical Science (CMB), University of Lleida & IRBLleida, 2Department of Computers an Industrial Engineering (DIEI), University of Lleida, Lleida and 3Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[{"name":"1 Department of Basic Medical Science (CMB), University of Lleida & IRBLleida, 2Department of Computers an Industrial Engineering (DIEI), University of Lleida, Lleida and 3Structural Biology and Biocomputing Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2013,11,13]]},"reference":[{"key":"2023012710454311800_btt639-B2","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1758-2946-3-41","article-title":"OSCAR4: a flexible architecture for chemical text-mining","volume":"3","author":"Jessop","year":"2011","journal-title":"J. Cheminform."},{"key":"2023012710454311800_btt639-B3","doi-asserted-by":"crossref","first-page":"i268","DOI":"10.1093\/bioinformatics\/btn181","article-title":"Detection of IUPAC and IUPAC-like chemical names","volume":"24","author":"Klinger","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012710454311800_btt639-B4","article-title":"Chemical names: terminological resources and corpora annotation","volume-title":"Proceedings of Workshop on Building and Evaluating Resources for Biomedical Text Mining","author":"Kol\u00e1\u0159ik","year":"2008"},{"key":"2023012710454311800_btt639-B5","first-page":"282","article-title":"Conditional random fields: probabilistic models for segmenting and labeling sequence data","volume-title":"Proceedings of the Eighteenth International Conference on Machine Learning (ICML 2001)","author":"Lafferty","year":"2001"},{"key":"2023012710454311800_btt639-B6","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1016\/j.drudis.2010.10.003","article-title":"PubChem as a public resource for drug discovery","volume":"15","author":"Li","year":"2010","journal-title":"Drug Discov. Today"},{"key":"2023012710454311800_btt639-B7","volume-title":"IUPAC Compendium of Chemical Terminology. Gold Book","author":"McNaught","year":"1997","edition":"2nd edn"},{"key":"2023012710454311800_btt639-B8","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1093\/bioinformatics\/bts183","article-title":"ChemSpot: a hybrid system for chemical named entity recognition","volume":"28","author":"Rockt\u00e4schel","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012710454311800_btt639-B9","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/gb-2008-9-s2-s2","article-title":"Overview of BioCreative II gene mention recognition","volume":"9","author":"Smith","year":"2008","journal-title":"Genome Biol."},{"key":"2023012710454311800_btt639-B10","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1002\/minf.201100005","article-title":"Text mining for drugs and chemical compounds: methods, tools and applications","volume":"30","author":"Vazquez","year":"2011","journal-title":"Mol. Inform."},{"key":"2023012710454311800_btt639-B11","doi-asserted-by":"crossref","first-page":"D901","DOI":"10.1093\/nar\/gkm958","article-title":"DrugBank: a knowledgebase for drugs, drug actions and drug targets","volume":"36","author":"Wishart","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1039\/48921652\/bioinformatics_30_7_1039.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1039\/48921652\/bioinformatics_30_7_1039.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:19:28Z","timestamp":1674818368000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/7\/1039\/232447"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,13]]},"references-count":10,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2014,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt639","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,4,1]]},"published":{"date-parts":[[2013,11,13]]}}}