{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,27]],"date-time":"2024-04-27T11:17:58Z","timestamp":1714216678769},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,15]],"date-time":"2019-11-15T00:00:00Z","timestamp":1573776000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish Ministry of Economy and Competitiveness"},{"name":"Maria de Maeztu Units of Excellence Programme","award":["MDM-2015-0502"]},{"name":"CROSSTEXT","award":["TIN2015-72646-EXP","MINECO\/FEDER"]},{"name":"DeepReading","award":["RTI2018-096846-B-C21 MCIU\/AEI\/FEDER"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Biomedical literature is one of the most relevant sources of information for knowledge mining in the field of Bioinformatics. In spite of English being the most widely addressed language in the field; in recent years, there has been a growing interest from the natural language processing community in dealing with languages other than English. However, the availability of language resources and tools for appropriate treatment of non-English texts is lacking behind. Our research is concerned with the semantic annotation of biomedical texts in the Spanish language, which can be considered an under-resourced language where biomedical text processing is concerned.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We have carried out experiments to assess the effectiveness of several methods for the automatic annotation of biomedical texts in Spanish. One approach is based on the linguistic analysis of Spanish texts and their annotation using an information retrieval and concept disambiguation approach. A second method takes advantage of a Spanish\u2013English machine translation process to annotate English documents and transfer annotations back to Spanish. A third method takes advantage of the combination of both procedures. Our evaluation shows that a combined system has competitive advantages over the two individual procedures.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n UMLSMapper (https:\/\/snlt.vicomtech.org\/umlsmapper) and the annotation transfer tool (http:\/\/scientmin.taln.upf.edu\/anntransfer\/) are freely available for research purposes as web services and\/or demos.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz853","type":"journal-article","created":{"date-parts":[[2019,11,13]],"date-time":"2019-11-13T12:10:43Z","timestamp":1573647043000},"page":"1872-1880","source":"Crossref","is-referenced-by-count":8,"title":["Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-8648-0428","authenticated-orcid":false,"given":"Naiara","family":"Perez","sequence":"first","affiliation":[{"name":"Vicomtech , SNLT, Donostia 20009, Spain"}]},{"given":"Pablo","family":"Accuosto","sequence":"additional","affiliation":[{"name":"Barcelona, TALN\/DTIC, Universitat Pompeu Fabra , Barcelona 08018, Spain"}]},{"given":"\u00c0lex","family":"Bravo","sequence":"additional","affiliation":[{"name":"Barcelona, TALN\/DTIC, Universitat Pompeu Fabra , Barcelona 08018, Spain"}]},{"given":"Montse","family":"Cuadros","sequence":"additional","affiliation":[{"name":"Vicomtech , SNLT, Donostia 20009, Spain"}]},{"given":"Eva","family":"Mart\u00ednez-Garcia","sequence":"additional","affiliation":[{"name":"Vicomtech , SNLT, Donostia 20009, Spain"}]},{"given":"Horacio","family":"Saggion","sequence":"additional","affiliation":[{"name":"Barcelona, TALN\/DTIC, Universitat Pompeu Fabra , Barcelona 08018, Spain"}]},{"given":"German","family":"Rigau","sequence":"additional","affiliation":[{"name":"IXA Group, HiTZ Centre, University of the Basque Country UPV\/EHU , Donostia 20018, Spain"}]}],"member":"286","published-online":{"date-parts":[[2019,11,15]]},"reference":[{"key":"2023060912003898800_btz853-B1","first-page":"57","article-title":"Improving the accessibility of biomedical texts by semantic enrichment and definition expansion","volume":"61","author":"Accuosto","year":"2018","journal-title":"Revista de PLN"},{"key":"2023060912003898800_btz853-B2","first-page":"3823","author":"Agerri","year":"2014"},{"key":"2023060912003898800_btz853-B3","first-page":"33","author":"Agirre","year":"2009"},{"key":"2023060912003898800_btz853-B4","first-page":"17","author":"Aronson","year":"2001"},{"key":"2023060912003898800_btz853-B5","first-page":"1","volume-title":"MetaMap: Mapping Text to the UMLS Metathesaurus","author":"Aronson","year":"2006"},{"key":"2023060912003898800_btz853-B6","author":"Attardi","year":"2013"},{"key":"2023060912003898800_btz853-B7","author":"Bahdanau","year":"2015"},{"key":"2023060912003898800_btz853-B8","first-page":"247","article-title":"Semantic annotation of biomedical texts through concept retrieval","volume":"45","author":"Berlanga","year":"2010","journal-title":"Revista de PLN"},{"key":"2023060912003898800_btz853-B9","author":"Bodnari","year":"2013"},{"key":"2023060912003898800_btz853-B10","first-page":"135","article-title":"Enriching word vectors with subword information","volume":"5","author":"Bojanowski","year":"2017","journal-title":"Trans. Assoc. Comput. Ling"},{"key":"2023060912003898800_btz853-B11","first-page":"346","author":"Carrero","year":"2008"},{"key":"2023060912003898800_btz853-B12","first-page":"751","author":"Castro","year":"2010"},{"key":"2023060912003898800_btz853-B13","first-page":"1724","author":"Cho","year":"2014"},{"key":"2023060912003898800_btz853-B14","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1177\/001316446002000104","article-title":"A coefficient of agreement for nominal scales","volume":"20","author":"Cohen","year":"1960","journal-title":"Educ. Psychol. Meas"},{"key":"2023060912003898800_btz853-B15","first-page":"322","author":"Cuadros","year":"2018"},{"key":"2023060912003898800_btz853-B16","first-page":"21","article-title":"An efficient solution for mapping free text to ontology terms","author":"Dai","year":"2008","journal-title":"AMIA Summit Transl. Bioinf."},{"key":"2023060912003898800_btz853-B17","doi-asserted-by":"crossref","first-page":"D492","DOI":"10.1093\/nar\/gkp858","article-title":"The NCBI biosystems database","volume":"38","author":"Geer","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023060912003898800_btz853-B18","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The gene ontology (GO) database and informatics resource","volume":"32","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023060912003898800_btz853-B19","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkh023","article-title":"The microRNA registry","volume":"32","author":"GriffithsJones","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023060912003898800_btz853-B20","doi-asserted-by":"crossref","first-page":"D1214","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: improved services and an expanding collection of metabolites","volume":"44","author":"Hastings","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023060912003898800_btz853-B21","first-page":"517","author":"Haveliwala","year":"2002"},{"key":"2023060912003898800_btz853-B22","first-page":"280","author":"Intxaurrondo","year":"2018"},{"key":"2023060912003898800_btz853-B23","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1111\/j.1469-8137.1912.tb05611.x","article-title":"The distribution of the flora in the alpine zone","volume":"11","author":"Jaccard","year":"1912","journal-title":"New Phytol"},{"key":"2023060912003898800_btz853-B24","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1093\/jamia\/ocv037","article-title":"A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC","volume":"22","author":"Kors","year":"2015","journal-title":"J. Am. Med. Inf. Assoc"},{"key":"2023060912003898800_btz853-B25","first-page":"55","author":"Manning","year":"2014"},{"key":"2023060912003898800_btz853-B26","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1055\/s-0038-1634592","article-title":"The representation of meaning in the UMLS","volume":"34","author":"McCray","year":"1995","journal-title":"Methods Inf. Med"},{"key":"2023060912003898800_btz853-B27","first-page":"2942","author":"Neves","year":"2016"},{"key":"2023060912003898800_btz853-B28","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1093\/bioinformatics\/btt317","article-title":"BeCAS: biomedical concept recognition services and visualization","volume":"29","author":"Nunes","year":"2013","journal-title":"Bioinformatics"},{"key":"2023060912003898800_btz853-B29","first-page":"536","author":"Oronoz","year":"2013"},{"key":"2023060912003898800_btz853-B30","first-page":"311","author":"Papineni","year":"2002"},{"key":"2023060912003898800_btz853-B31","first-page":"2045","author":"Perez","year":"2018"},{"key":"2023060912003898800_btz853-B32","first-page":"353","author":"Rebholz-Schuhmann","year":"2013"},{"key":"2023060912003898800_btz853-B33","doi-asserted-by":"crossref","first-page":"e75185","DOI":"10.1371\/journal.pone.0075185","article-title":"Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)","volume":"8","author":"Rebholz-Schuhmann","year":"2013","journal-title":"PLoS One"},{"key":"2023060912003898800_btz853-B34","first-page":"16","author":"Roller","year":"2018"},{"key":"2023060912003898800_btz853-B35","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1136\/jamia.2009.001560","article-title":"Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications","volume":"17","author":"Savova","year":"2010","journal-title":"J. Am. Med. Inf. Assoc"},{"key":"2023060912003898800_btz853-B36","first-page":"1715","author":"Sennrich","year":"2016"},{"key":"2023060912003898800_btz853-B37","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1093\/jamia\/ocx132","article-title":"CLAMP\u2014a toolkit for efficiently building customized clinical natural language processing pipelines","volume":"25","author":"Soysal","year":"2017","journal-title":"J. Am. Med. Inf. Assoc"},{"key":"2023060912003898800_btz853-B38","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/s12859-015-0871-y","article-title":"NOBLE\u2013flexible concept recognition for large-scale biomedical natural language processing","volume":"17","author":"Tseytlin","year":"2016","journal-title":"BMC Bioinf"},{"key":"2023060912003898800_btz853-B39","author":"Ware","year":"2015"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz853\/30795582\/btz853.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/6\/1872\/50554323\/bioinformatics_36_6_1872.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/6\/1872\/50554323\/bioinformatics_36_6_1872.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,9]],"date-time":"2023-06-09T12:05:22Z","timestamp":1686312322000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/6\/1872\/5626183"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,11,15]]},"references-count":39,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2020,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz853","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,3,15]]},"published":{"date-parts":[[2019,11,15]]}}}