{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:38:38Z","timestamp":1740184718295,"version":"3.37.3"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,7,26]],"date-time":"2019-07-26T00:00:00Z","timestamp":1564099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC0910404"],"award-info":[{"award-number":["2018YFC0910404"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61772409"],"award-info":[{"award-number":["61772409"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100019069","name":"Chinese Academy of Engineering","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100019069","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A biochemical reaction, bio-event, depicts the relationships between participating entities. Current text mining research has been focusing on identifying bio-events from scientific literature. However, rare efforts have been dedicated to normalize bio-events extracted from scientific literature with the entries in the curated reaction databases, which could disambiguate the events and further support interconnecting events into biologically meaningful and complete networks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this paper, we propose BioNorm, a novel method of normalizing bio-events extracted from scientific literature to entries in the bio-molecular reaction database, e.g. IntAct. BioNorm considers event normalization as a paraphrase identification problem. It represents an entry as a natural language statement by combining multiple types of information contained in it. Then, it predicts the semantic similarity between the natural language statement and the statements mentioning events in scientific literature using a long short-term memory recurrent neural network (LSTM). An event will be normalized to the entry if the two statements are paraphrase. To the best of our knowledge, this is the first attempt of event normalization in the biomedical text mining. The experiments have been conducted using the molecular interaction data from IntAct. The results demonstrate that the method could achieve F-score of 0.87 in normalizing event-containing statements.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code is available at the gitlab repository https:\/\/gitlab.com\/BioAI\/leen and BioASQvec Plus is available on figshare https:\/\/figshare.com\/s\/45896c31d10c3f6d857a.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz571","type":"journal-article","created":{"date-parts":[[2019,7,24]],"date-time":"2019-07-24T11:27:00Z","timestamp":1563967620000},"page":"611-620","source":"Crossref","is-referenced-by-count":4,"title":["BioNorm: deep learning-based event normalization for the curation of reaction databases"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6683-0256","authenticated-orcid":false,"given":"Peiliang","family":"Lou","sequence":"first","affiliation":[{"name":"Department of Computer Science and Technology, School of Electronic and Information Engineering , Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi 710049, China"},{"name":"Key Laboratory of Intelligent Networks and Network Security (Xi\u2019an Jiaotong University), Ministry of Education , Xi\u2019an, Shaanxi 710049, China"}]},{"given":"Antonio","family":"Jimeno Yepes","sequence":"additional","affiliation":[{"name":"IBM Research Australia , Southbank, VIC 3006, Australia"}]},{"given":"Zai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Technology, School of Electronic and Information Engineering , Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi 710049, China"}]},{"given":"Qinghua","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Technology, School of Electronic and Information Engineering , Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi 710049, China"},{"name":"National Engineering Lab for Big Data Analytics , Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi 710049, China"}]},{"given":"Xiangrong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education , School of Artificial Intelligence, Xidian University, Xi'an, 710071, China"}]},{"given":"Chen","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Technology, School of Electronic and Information Engineering , Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi 710049, China"},{"name":"National Engineering Lab for Big Data Analytics , Xi\u2019an Jiaotong University, Xi\u2019an, Shaanxi 710049, China"}]}],"member":"286","published-online":{"date-parts":[[2019,7,26]]},"reference":[{"key":"2023013112070594700_btz571-B1","doi-asserted-by":"crossref","first-page":"25.","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023013112070594700_btz571-B2","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1162\/tacl_a_00051","article-title":"Enriching word vectors with subword information","volume":"5","author":"Bojanowski","year":"2017","journal-title":"Trans. Assoc. Comput. Linguist"},{"year":"2018","author":"Cer","key":"2023013112070594700_btz571-B3"},{"key":"2023013112070594700_btz571-B4","doi-asserted-by":"crossref","first-page":"baw101","DOI":"10.1093\/database\/baw101","article-title":"Pipe: a protein\u2013protein interaction passage extraction module for biocreative challenge","volume":"2016","author":"Chang","year":"2016","journal-title":"Database"},{"year":"2018","author":"Chen","key":"2023013112070594700_btz571-B5"},{"year":"2018","author":"Chen","key":"2023013112070594700_btz571-B6"},{"key":"2023013112070594700_btz571-B7","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1145\/2939672.2939785","volume-title":"Proceedings of the 22nd Acm Sigkdd International Conference on Knowledge Discovery and Data Mining","author":"Chen","year":"2016"},{"key":"2023013112070594700_btz571-B8","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1093\/nar\/gky092","article-title":"UniProt: the universal protein knowledgebase","volume":"46","year":"2018","journal-title":"Nucleic Acids Res"},{"year":"2019","author":"Devlin","key":"2023013112070594700_btz571-B9"},{"key":"2023013112070594700_btz571-B10","doi-asserted-by":"crossref","first-page":"bas020","DOI":"10.1093\/database\/bas020","article-title":"Text mining for the biocuration workflow","volume":"2012","author":"Hirschman","year":"2012","journal-title":"Database"},{"year":"2014","author":"Hu","key":"2023013112070594700_btz571-B11"},{"year":"2009","author":"Kim","key":"2023013112070594700_btz571-B12"},{"first-page":"1","year":"2011","author":"Kim","key":"2023013112070594700_btz571-B13"},{"key":"2023013112070594700_btz571-B14","doi-asserted-by":"crossref","first-page":"5339","DOI":"10.1074\/jbc.274.9.5339","article-title":"Purification and identification of a novel subunit of protein serine\/threonine phosphatase 4","volume":"274","author":"Kloeker","year":"1999","journal-title":"J. Biol. Chem"},{"key":"2023013112070594700_btz571-B15","doi-asserted-by":"crossref","first-page":"S4.","DOI":"10.1186\/gb-2008-9-s2-s4","article-title":"Overview of the protein\u2013protein interaction annotation extraction task of biocreative II","volume":"9","author":"Krallinger","year":"2008","journal-title":"Genome Biol"},{"year":"2019","author":"Lee","key":"2023013112070594700_btz571-B16"},{"key":"2023013112070594700_btz571-B17","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1093\/bib\/bbt006","article-title":"Biological network extraction from scientific literature: state of the art and challenges","volume":"15","author":"Li","year":"2014","journal-title":"Brief. Bioinf"},{"year":"2019","author":"Liu","key":"2023013112070594700_btz571-B18"},{"first-page":"3111","year":"2013","author":"Mikolov","key":"2023013112070594700_btz571-B19"},{"year":"2013","author":"Mikolov","key":"2023013112070594700_btz571-B20"},{"key":"2023013112070594700_btz571-B21","doi-asserted-by":"crossref","first-page":"D415","DOI":"10.1093\/nar\/gkw990","article-title":"Updates in rhea\u2013an expert curated resource of biochemical reactions","volume":"45","author":"Morgat","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013112070594700_btz571-B22","first-page":"2786","volume-title":"AAAI","author":"Mueller","year":"2016"},{"first-page":"1","year":"2013","author":"N\u00e9dellec","key":"2023013112070594700_btz571-B23"},{"key":"2023013112070594700_btz571-B24","first-page":"186","volume-title":"Biocomputing","author":"Orchard","year":"2005"},{"key":"2023013112070594700_btz571-B25","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkt1115","article-title":"The MIntAct project\u2013IntAct as a common curation platform for 11 molecular interaction databases","volume":"42","author":"Orchard","year":"2014","journal-title":"Nucleic Acids Res"},{"year":"2014","author":"Pavlopoulos","key":"2023013112070594700_btz571-B26"},{"year":"2015","author":"Rockt\u00e4schel","key":"2023013112070594700_btz571-B27"},{"year":"2018","author":"Talman","key":"2023013112070594700_btz571-B28"},{"key":"2023013112070594700_btz571-B29","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1007\/978-3-319-96136-1_12","volume-title":"International Conference on Machine Learning and Data Mining in Pattern Recognition","author":"Tawfik","year":"2018"},{"key":"2023013112070594700_btz571-B30","doi-asserted-by":"crossref","first-page":"D331","DOI":"10.1093\/nar\/gkw1108","article-title":"Expansion of the gene ontology knowledgebase and resources: the Gene Ontology Consortium","volume":"45","author":"Thomas","year":"2017","journal-title":"Nucleic Acids Res"},{"year":"2016","author":"Tulkens","key":"2023013112070594700_btz571-B31"},{"first-page":"6000","year":"2017","author":"Vaswani","key":"2023013112070594700_btz571-B32"},{"year":"2016","author":"Wang","key":"2023013112070594700_btz571-B33"},{"key":"2023013112070594700_btz571-B34","doi-asserted-by":"crossref","first-page":"W518","DOI":"10.1093\/nar\/gkt441","article-title":"PubTator: a web-based text mining tool for assisting biocuration","volume":"41","author":"Wei","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023013112070594700_btz571-B35","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s12911-018-0628-4","article-title":"Automatic extraction of protein\u2013protein interactions using grammatical relationship graph","volume":"18","author":"Yu","year":"2018","journal-title":"BMC Med. Inf. Decis. Mak"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz571\/29112973\/btz571.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/2\/611\/48991108\/btz571.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/2\/611\/48991108\/btz571.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T21:24:44Z","timestamp":1675200284000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/2\/611\/5539693"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,7,26]]},"references-count":35,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz571","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,1,15]]},"published":{"date-parts":[[2019,7,26]]}}}