{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T16:16:03Z","timestamp":1780762563756,"version":"3.54.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2018,9,19]],"date-time":"2018-09-19T00:00:00Z","timestamp":1537315200000},"content-version":"vor","delay-in-days":261,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ATT Tieto k\u00e4ytt\u00f6\u00f6n"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"DOI":"10.1093\/database\/bay096","type":"journal-article","created":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T11:32:21Z","timestamp":1534764741000},"source":"Crossref","is-referenced-by-count":16,"title":["Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling"],"prefix":"10.1093","volume":"2018","author":[{"given":"Suwisa","family":"Kaewphan","sequence":"first","affiliation":[{"name":"Turku Centre for Computer Science, Turku, Finland"},{"name":"Department of Future Technologies, University of Turku, Turku, Finland"},{"name":"University of Turku Graduate School, Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Hakala","sequence":"additional","affiliation":[{"name":"Department of Future Technologies, University of Turku, Turku, Finland"},{"name":"University of Turku Graduate School, Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niko","family":"Miekka","sequence":"additional","affiliation":[{"name":"Department of Future Technologies, University of Turku, Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tapio","family":"Salakoski","sequence":"additional","affiliation":[{"name":"Turku Centre for Computer Science, Turku, Finland"},{"name":"University of Turku Graduate School, Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Filip","family":"Ginter","sequence":"additional","affiliation":[{"name":"Department of Future Technologies, University of Turku, Turku, Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,18]]},"reference":[{"key":"key\n\t\t\t\t20180920011209_ref1","doi-asserted-by":"crossref","first-page":"12","DOI":"10.18653\/v1\/W16-3002","article-title":"Overview of the bacteria biotope task at BioNLP shared task 2016","author":"Del\u0117ger","year":"2016","journal-title":"Proceedings of the 4th BioNLP Shared Task Workshop, Berlin, Germany"},{"key":"key\n\t\t\t\t20180920011209_ref2","first-page":"70","article-title":"Introduction to the bio-entity recognition task at JNLPBA","volume-title":"Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, University of Geneva, Switzerland, 28\u201329 August 2004","author":"Kim","year":"2004"},{"key":"key\n\t\t\t\t20180920011209_ref3","first-page":"28","article-title":"Bio-ID track overview","author":"Arighi","year":"2017","journal-title":"Proceedings of BioCreative VI Workshop, Bethesda, MD, USA"},{"key":"key\n\t\t\t\t20180920011209_ref4","first-page":"1","article-title":"pGenN, a gene normalization tool for plant genes and proteins in scientific literature","volume":"10","author":"Ding","year":"2015","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180920011209_ref5","doi-asserted-by":"crossref","first-page":"i48","DOI":"10.1093\/bioinformatics\/btx228","article-title":"Deep learning with word embeddings improves biomedical named entity recognition","volume":"33","author":"Habibi","year":"2017","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180920011209_ref6","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1093\/bioinformatics\/btv570","article-title":"Cell line name recognition in support of the identification of synthetic lethality in cancer from text","volume":"32","author":"Kaewphan","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180920011209_ref7","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1093\/bioinformatics\/btt580","article-title":"Anatomical entity mention recognition at literature scale","volume":"30","author":"Pyysalo","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180920011209_ref8","first-page":"80","article-title":"End-to-end system for bacteria habitat extraction","author":"Mehryary","year":"2017","journal-title":"Proceedings of the 16th BioNLP Workshop, Vancouver, Canada, 4 August 2017"},{"key":"key\n\t\t\t\t20180920011209_ref9","first-page":"1","article-title":"GNormPlus: an integrative approach for tagging genes, gene families, and protein domains","author":"Wei","year":"2015","journal-title":"Biomed Res. Int."},{"key":"key\n\t\t\t\t20180920011209_ref10","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1186\/s12859-017-1805-7","article-title":"CNN-based ranking for biomedical entity normalization","volume":"18","author":"Li","year":"2017","journal-title":"BMC Bioinf."},{"key":"key\n\t\t\t\t20180920011209_ref11","first-page":"10","article-title":"Normalising medical concepts in social media texts by learning semantic representation","author":"Limsopatham","year":"2016","journal-title":"Proceedings of the Fifth Workshops on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2016), Osaka, Japan, 12 December 2016"},{"key":"key\n\t\t\t\t20180920011209_ref12","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1093\/bioinformatics\/btw343","article-title":"TaggerOne: joint named entity recognition and normalization with semi-Markov Models","volume":"32","author":"Leaman","year":"2016","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180920011209_ref13","first-page":"24","article-title":"A neural named entity recognition approach to biological entity identification","author":"Sheng","year":"2017","journal-title":"Proceedings of the BioCreative VI Workshop"},{"key":"key\n\t\t\t\t20180920011209_ref14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/database\/bay048","article-title":"SPRENO: a BioC module for identifying organism terms in figure captions","volume":"2018","author":"Dai","year":"2018","journal-title":"Database"},{"key":"key\n\t\t\t\t20180920011209_ref15","first-page":"32","article-title":"TurkuNLP entry for interactive Bio-ID assignment","author":"Kaewphan","year":"2017","journal-title":"Proceedings of the BioCreative VI Workshop"},{"key":"key\n\t\t\t\t20180920011209_ref16","first-page":"39","article-title":"Distributional semantics resources for biomedical text processing","author":"Pyysalo","year":"2013","journal-title":"Proceedings of the 5th International Symposium on Languages in Biology and Medicine,"},{"key":"key\n\t\t\t\t20180920011209_ref17","first-page":"209","article-title":"AKANE system: protein-protein interaction pairs in BioCreAtIvE2 challenge, PPI-IPS subtask","author":"Saetre","year":"2007","journal-title":"Proceedings of the Second Biocreative Challenge Evaluation Workshop,"},{"key":"key\n\t\t\t\t20180920011209_ref18","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1007\/11573036_36","article-title":"Developing a robust part-of-speech tagger for biomedical text","volume-title":"Advances in Informatics: 10th Panhellenic Conference on Informatics, PCI, Valos, Greece, 11\u201313 November 2005","author":"Tsuruoka","year":"2005"},{"key":"key\n\t\t\t\t20180920011209_ref19","doi-asserted-by":"crossref","first-page":"D350","DOI":"10.1093\/nar\/gkm791","article-title":"ChEBI: a database and ontology for chemical entities of biological interest","volume":"36","author":"Degtyarenko","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180920011209_ref20","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/S1574-1400(08)00012-1","article-title":"PubChem: integrated platform of small molecules and biological activities","volume":"4","author":"Bolton","year":"2008","journal-title":"Annu. Rep. Comput. Chem."},{"key":"key\n\t\t\t\t20180920011209_ref21","first-page":"D42","article-title":"Gene: a gene-centered information resource at NCBI","volume":"43","author":"Brown","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180920011209_ref22","first-page":"D204","article-title":"UniProt: a hub for protein information","author":"UniProt Consortium","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180920011209_ref23","first-page":"D143","article-title":"The NCBI taxonomy database","volume":"40","author":"Federhen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180920011209_ref24","doi-asserted-by":"crossref","first-page":"R5","DOI":"10.1186\/gb-2012-13-1-r5","article-title":"Uberon, an integrative multi-species anatomy ontology","volume":"13","author":"Mungall","year":"2012","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180920011209_ref25","doi-asserted-by":"crossref","first-page":"D261","DOI":"10.1093\/nar\/gkh036","article-title":"The Gene Ontology (GO) database and informatics resource","volume":"32","author":"Gene Ontology Consortium","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180920011209_ref26","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1007\/s007050050642","article-title":"Abbreviations for invertebrate virus species names","volume":"144","author":"Fauquet","year":"1999","journal-title":"Arch. Virol."},{"key":"key\n\t\t\t\t20180920011209_ref27","doi-asserted-by":"crossref","DOI":"10.3115\/1119176.1119204","article-title":"Named entity recognition with character-level models","volume-title":"Proceedings of the Seventh Conference on Natural Language Learning at HLT-NAACL 2003-Volume 4, Edmonton, Canada, 31 May 2003","author":"Klein","year":"2003"},{"key":"key\n\t\t\t\t20180920011209_ref28","article-title":"Charner: character-level named entity recognition","author":"Kuru","year":"2016","journal-title":"Proceedings of COLING 2016, the 26th International Conference on Computational Linguistics: Technical Papers, Osaka, Japan, 11\u201316 December 2016"},{"key":"key\n\t\t\t\t20180920011209_ref29","first-page":"1064","article-title":"End-to-end sequence labeling via bi-directional LSTM-CNNs-CRF","volume-title":"Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, Berlin, Germany, 7\u201312 August 2016","author":"Ma","year":"2016"},{"key":"key\n\t\t\t\t20180920011209_ref30","first-page":"851","article-title":"Simple and efficient algorithm for approximate dictionary matching","volume-title":"Proceedings of the 23rd International Conference on Computational Linguistics","author":"Okazaki","year":"2010"},{"key":"key\n\t\t\t\t20180920011209_ref31","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1186\/1471-2105-9-402","article-title":"Abbreviation definition identification based on automatic precision estimates","volume":"9","author":"Sohn","year":"2008","journal-title":"BMC Bioinf."},{"key":"key\n\t\t\t\t20180920011209_ref32","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1093\/bioinformatics\/bth496","article-title":"Gene name ambiguity of eukaryotic nomenclatures","volume":"21","author":"Chen","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180920011209_ref33","first-page":"28","article-title":"EVEX: a PubMed-scale resource for homology-based generalization of text mining predictions","volume-title":"Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, Portland, Oregon, USA, 23\u201324 June 2011","author":"Van Landeghem","year":"2011"},{"key":"key\n\t\t\t\t20180920011209_ref34","first-page":"28","article-title":"SPRENO: A BioC module for recognizing and normalizing species and their model organisms","author":"Singh","year":"2017","journal-title":"Proceedings of the BioCreative VI Workshop, Bethesda, MD, USA"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/bay096\/25811111\/bay096.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,4]],"date-time":"2023-09-04T12:50:06Z","timestamp":1693831806000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/bay096\/5101499"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,1]]},"references-count":34,"URL":"https:\/\/doi.org\/10.1093\/database\/bay096","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018]]},"published":{"date-parts":[[2018,1,1]]}}}