{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T05:22:36Z","timestamp":1784956956885,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2022,9,2]],"date-time":"2022-09-02T00:00:00Z","timestamp":1662076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2020R1A2C3010638"],"award-info":[{"award-number":["NRF-2020R1A2C3010638"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2014M3C9A3063541"],"award-info":[{"award-number":["NRF-2014M3C9A3063541"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministry of Health & Welfare, Republic of Korea","award":["HR20C0021"],"award-info":[{"award-number":["HR20C0021"]}]},{"name":"ICT Creative Consilience program","award":["IITP-2021-0-01819"],"award-info":[{"award-number":["IITP-2021-0-01819"]}]},{"name":"IITP (Institute for Information & communications Technology Planning & Evaluation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,14]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>\u2003<\/jats:title><jats:p>In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>Web service of BERN2 is publicly available at http:\/\/bern2.korea.ac.kr. We also provide local installation of BERN2 at https:\/\/github.com\/dmis-lab\/BERN2.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac598","type":"journal-article","created":{"date-parts":[[2022,8,31]],"date-time":"2022-08-31T12:04:08Z","timestamp":1661947448000},"page":"4837-4839","source":"Crossref","is-referenced-by-count":111,"title":["BERN2: an advanced neural biomedical named entity recognition and normalization tool"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7978-8114","authenticated-orcid":false,"given":"Mujeen","family":"Sung","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, Korea University , Seoul 02841, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1346-730X","authenticated-orcid":false,"given":"Minbyul","family":"Jeong","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Korea University , Seoul 02841, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5709-9898","authenticated-orcid":false,"given":"Yonghwa","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Korea University , Seoul 02841, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8224-8354","authenticated-orcid":false,"given":"Donghyeon","family":"Kim","sequence":"additional","affiliation":[{"name":"AIRS Company, Hyundai Motor Group , Seoul 06620, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4972-239X","authenticated-orcid":false,"given":"Jinhyuk","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Korea University , Seoul 02841, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6798-9106","authenticated-orcid":false,"given":"Jaewoo","family":"Kang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, Korea University , Seoul 02841, Republic of Korea"},{"name":"AIGEN Sciences , Seoul 04778, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,2]]},"reference":[{"key":"2022101415200379000_btac598-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jbi.2013.12.006","article-title":"NCBI disease corpus: a resource for disease name recognition and concept normalization","volume":"47","author":"Do\u011fan","year":"2014","journal-title":"J. Biomed. Informatics"},{"key":"2022101415200379000_btac598-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":"2022101415200379000_btac598-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/3458754","article-title":"Domain-specific language model pretraining for biomedical natural language processing","volume":"3","author":"Gu","year":"2022","journal-title":"ACM Trans. Comput. Healthcare (HEALTH)"},{"key":"2022101415200379000_btac598-B4","doi-asserted-by":"crossref","first-page":"73729","DOI":"10.1109\/ACCESS.2019.2920708","article-title":"A neural named entity recognition and multi-type normalization tool for biomedical text mining","volume":"7","author":"Kim","year":"2019","journal-title":"IEEE Access"},{"key":"2022101415200379000_btac598-B5","author":"Kim","year":"2004"},{"key":"2022101415200379000_btac598-B6","author":"K\u00f6ksal","year":"2020"},{"key":"2022101415200379000_btac598-B7","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1758-2946-7-S1-S2","article-title":"The CHEMDNER corpus of chemicals and drugs and its annotation principles","volume":"7","author":"Krallinger","year":"2015","journal-title":"J. Cheminform"},{"key":"2022101415200379000_btac598-B8","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":"2022101415200379000_btac598-B9","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btz682","article-title":"BioBERT: a pre-trained biomedical language representation model for biomedical text mining","author":"Lee","year":"2020","journal-title":"Bioinformatics"},{"key":"2022101415200379000_btac598-B10","author":"Lewis","year":"2020"},{"key":"2022101415200379000_btac598-B11","article-title":"Overview of biocreative II gene mention recognition","volume":"9, S2","author":"Smith","year":"2008","journal-title":"Genome Biol"},{"key":"2022101415200379000_btac598-B12","first-page":"3641","author":"Sung","year":"2020"},{"key":"2022101415200379000_btac598-B13","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1093\/bioinformatics\/bty869","article-title":"Cross-type biomedical named entity recognition with deep multi-task learning","volume":"35","author":"Wang","year":"2019","journal-title":"Bioinformatics"},{"key":"2022101415200379000_btac598-B14","doi-asserted-by":"crossref","first-page":"2792","DOI":"10.1093\/bioinformatics\/btab042","article-title":"Hunflair: an easy-to-use tool for state-of-the-art biomedical named entity recognition","volume":"37","author":"Weber","year":"2021","journal-title":"Bioinformatics"},{"key":"2022101415200379000_btac598-B15","doi-asserted-by":"crossref","first-page":"918710","DOI":"10.1155\/2015\/918710","article-title":"Gnormplus: an integrative approach for tagging genes, gene families, and protein domains","volume":"2015","author":"Wei","year":"2015","journal-title":"Biomed Res. Int"},{"key":"2022101415200379000_btac598-B16","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1093\/bioinformatics\/btx541","article-title":"tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine","volume":"34","author":"Wei","year":"2018","journal-title":"Bioinformatics"},{"key":"2022101415200379000_btac598-B17","doi-asserted-by":"crossref","first-page":"W587","DOI":"10.1093\/nar\/gkz389","article-title":"PubTator Central: automated concept annotation for biomedical full text articles","volume":"47","author":"Wei","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022101415200379000_btac598-B18","doi-asserted-by":"crossref","DOI":"10.1038\/s41597-020-0543-2","article-title":"Building a PubMed knowledge graph","volume":"7","author":"Xu","year":"2020","journal-title":"Sci. Data"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac598\/45958172\/btac598.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/20\/4837\/46535173\/btac598.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/20\/4837\/46535173\/btac598.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,16]],"date-time":"2023-02-16T19:05:28Z","timestamp":1676574328000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/20\/4837\/6687126"}},"subtitle":[],"editor":[{"given":"Karsten","family":"Borgwardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,9,2]]},"references-count":18,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2022,9,2]]},"published-print":{"date-parts":[[2022,10,14]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac598","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,10,15]]},"published":{"date-parts":[[2022,9,2]]}}}