{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T15:24:43Z","timestamp":1769095483116,"version":"3.49.0"},"reference-count":59,"publisher":"Oxford University Press (OUP)","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Database"],"published-print":{"date-parts":[[2016]]},"DOI":"10.1093\/database\/baw161","type":"journal-article","created":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T15:05:49Z","timestamp":1479308749000},"page":"baw161","source":"Crossref","is-referenced-by-count":35,"title":["Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges"],"prefix":"10.1093","volume":"2016","author":[{"given":"Ayush","family":"Singhal","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Leaman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie","family":"Catlett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Lemberger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johanna","family":"McEntyre","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shawn","family":"Polson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia","family":"Arighi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,12,26]]},"reference":[{"key":"2016122618203570000_2016.0.baw161.1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku989"},{"key":"2016122618203570000_2016.0.baw161.2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1130"},{"key":"2016122618203570000_2016.0.baw161.3","doi-asserted-by":"crossref","unstructured":"Baxevanis A.D. Bateman A. (2006) The importance of biological databases in biological discovery. Curr. Protoc. Bioinformatics, 50, 1.1.1.\u20131.1.8.","DOI":"10.1002\/0471250953.bi0101s50"},{"key":"2016122618203570000_2016.0.baw161.4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt441"},{"key":"2016122618203570000_2016.0.baw161.5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1061"},{"key":"2016122618203570000_2016.0.baw161.6","doi-asserted-by":"publisher","DOI":"10.1002\/msb.201305048"},{"key":"2016122618203570000_2016.0.baw161.7","doi-asserted-by":"crossref","unstructured":"Hirschman L. Burns G.A. Krallinger M. . (2012) Text mining for the biocuration workflow. Database (Oxford), 2012, bas020.","DOI":"10.1093\/database\/bas020"},{"key":"2016122618203570000_2016.0.baw161.8","doi-asserted-by":"crossref","unstructured":"Lu Z. Hirschman L. (2012) Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. Database (Oxford), 2012, bas043.","DOI":"10.1093\/database\/bas043"},{"key":"2016122618203570000_2016.0.baw161.9","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-228"},{"key":"2016122618203570000_2016.0.baw161.10","doi-asserted-by":"crossref","unstructured":"Van Auken K. Fey P. Berardini T.Z. . (2012) Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database (Oxford), 2012, bas040.","DOI":"10.1093\/database\/bas040"},{"key":"2016122618203570000_2016.0.baw161.11","doi-asserted-by":"crossref","unstructured":"Wei C.H. Harris B.R. Li D. . (2012) Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford), 2012, bas041.","DOI":"10.1093\/database\/bas041"},{"key":"2016122618203570000_2016.0.baw161.12","doi-asserted-by":"crossref","unstructured":"Tudor C.O. Arighi C.N. Wang Q. . (2012) The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database (Oxford), 2012, bas044.","DOI":"10.1093\/database\/bas044"},{"key":"2016122618203570000_2016.0.baw161.13","doi-asserted-by":"crossref","unstructured":"Cejuela J.M. McQuilton P. Ponting L. . (2014) tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford), 2014, bau033.","DOI":"10.1093\/database\/bau033"},{"key":"2016122618203570000_2016.0.baw161.14","doi-asserted-by":"crossref","first-page":"S4.","DOI":"10.1186\/1471-2105-12-S8-S4","article-title":"BioCreative III interactive task: an overview","volume":"12","author":"Arighi","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2016122618203570000_2016.0.baw161.15","doi-asserted-by":"crossref","unstructured":"Arighi C.N. Carterette B. Cohen K.B. . (2013) An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database (Oxford), 2013, bas056.","DOI":"10.1093\/database\/bas056"},{"key":"2016122618203570000_2016.0.baw161.16","unstructured":"Matis-Mitchell S. Roberts P. Tudor C.O. Arighi C.N. (2013) BioCreative IV interactive task. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, vol 1. Bethesda, MD, pp. 190\u2013203."},{"key":"2016122618203570000_2016.0.baw161.17","doi-asserted-by":"crossref","unstructured":"Wang Q.H. Abdul S.S. Almeida L. . (2016) Overview of the interactive task in BioCreative V. Database (Oxford), 2016, baw119.","DOI":"10.1093\/database\/baw119"},{"key":"2016122618203570000_2016.0.baw161.18","doi-asserted-by":"crossref","unstructured":"Liechti R. George N. El-Gebali S. . (2016) SourceData - a semantic platform for curating and searching figures. bioRxiv, 058529.","DOI":"10.1101\/058529"},{"key":"2016122618203570000_2016.0.baw161.19","first-page":"321","article-title":"Leveraging web intelligence for finding interesting research datasets. Proceedings of the International Joint Conferences on Web Intelligence (WI) and Intelligent Agent Technologies (IAT)","volume":"1","author":"Singhal","year":"2013","journal-title":"2013 IEEE\/WIC\/ACM. IEEE"},{"key":"2016122618203570000_2016.0.baw161.20","unstructured":"Singhal A. (2014) Leveraging Open Source Web Resources to Improve Retrieval of Low Text Content Items. Department of Computer science. University of Minnesota, Minneapolis, MN, 144."},{"key":"2016122618203570000_2016.0.baw161.21","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-6-54"},{"key":"2016122618203570000_2016.0.baw161.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.taap.2013.07.007"},{"key":"2016122618203570000_2016.0.baw161.23","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-340"},{"key":"2016122618203570000_2016.0.baw161.24","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bav030"},{"key":"2016122618203570000_2016.0.baw161.25","unstructured":"Fluck J. Madan S. Ansari S. . (2014) BELIEF-a Semiautomatic Workflow for BEL Network Creation. Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM), University of Aveiro, Portugal, 109\u2013113."},{"key":"2016122618203570000_2016.0.baw161.26","doi-asserted-by":"crossref","first-page":"532.","DOI":"10.1038\/ismej.2015.252","article-title":"Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp","volume":"10","author":"Gomez","year":"2016","journal-title":"ISME J"},{"key":"2016122618203570000_2016.0.baw161.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.04.011"},{"key":"2016122618203570000_2016.0.baw161.28","doi-asserted-by":"crossref","first-page":"S28","DOI":"10.1513\/AnnalsATS.201306-161MG","article-title":"Mucosal immunity and the microbiome","volume":"11","author":"Neish","year":"2014","journal-title":"Ann. Am. Thoracic Soc"},{"key":"2016122618203570000_2016.0.baw161.29","doi-asserted-by":"publisher","DOI":"10.1111\/imm.12231"},{"key":"2016122618203570000_2016.0.baw161.30","doi-asserted-by":"publisher","DOI":"10.1038\/nature11234"},{"key":"2016122618203570000_2016.0.baw161.31","doi-asserted-by":"publisher","DOI":"10.1038\/nature13398"},{"key":"2016122618203570000_2016.0.baw161.32","doi-asserted-by":"crossref","first-page":"421\u2013433.","DOI":"10.4056\/sigs.2945050","article-title":"VIROME: a standard operating procedure for analysis of viral metagenome sequences","volume":"6","author":"Wommack","year":"2012","journal-title":"Stand. Genomic Sci"},{"key":"2016122618203570000_2016.0.baw161.33","unstructured":"Glass E.M. Wilkening J. Wilke A. . (2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb. Protoc., 2010, pdb. prot5368."},{"key":"2016122618203570000_2016.0.baw161.34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.1.35"},{"key":"2016122618203570000_2016.0.baw161.35","doi-asserted-by":"crossref","unstructured":"Pafilis E. Buttigieg P.L. Ferrell B. . (2016) EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database (Oxford), 2016.","DOI":"10.1093\/database\/baw005"},{"key":"2016122618203570000_2016.0.baw161.36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv045"},{"key":"2016122618203570000_2016.0.baw161.37","doi-asserted-by":"publisher","DOI":"10.1186\/2041-1480-4-43"},{"key":"2016122618203570000_2016.0.baw161.38","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw343"},{"key":"2016122618203570000_2016.0.baw161.39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0038460"},{"key":"2016122618203570000_2016.0.baw161.40","doi-asserted-by":"crossref","unstructured":"Wiegers T.C. Davis A.P. Mattingly C.J. (2014) Web services-based text-mining demonstrates broad impacts for interoperability and process simplification. Database (Oxford), 2014, bau050.","DOI":"10.1093\/database\/bau050"},{"key":"2016122618203570000_2016.0.baw161.41","doi-asserted-by":"publisher","DOI":"10.1017\/S1351324904003523"},{"key":"2016122618203570000_2016.0.baw161.42","unstructured":"Verspoor K. Baumgartner W. Jr Roeder C. . (2009) Abstracting the types away from a UIMA type system. In C. Chiarcos, R. Eckhart de Castilho, M. Stede (Eds.), Form to Meaning: Processing Texts Automatically, pp. 249\u2013256."},{"key":"2016122618203570000_2016.0.baw161.43","doi-asserted-by":"crossref","unstructured":"Comeau D.C. Islamaj Dogan R. Ciccarese P. . (2013) BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford), 2013, bat064.","DOI":"10.1093\/database\/bat064"},{"key":"2016122618203570000_2016.0.baw161.44","doi-asserted-by":"crossref","unstructured":"Comeau D.C. Batista-Navarro R.T. Dai H.J. . (2014) BioC interoperability track overview. Database (Oxford), 2014, bau053.","DOI":"10.1093\/database\/bau053"},{"key":"2016122618203570000_2016.0.baw161.45","doi-asserted-by":"publisher","DOI":"10.1038\/nbt0609-508"},{"key":"2016122618203570000_2016.0.baw161.46","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv760"},{"key":"2016122618203570000_2016.0.baw161.47","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-85"},{"key":"2016122618203570000_2016.0.baw161.48","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts332"},{"key":"2016122618203570000_2016.0.baw161.49","doi-asserted-by":"crossref","first-page":"e12704.","DOI":"10.1371\/journal.pone.0012704","article-title":"Systematic characterizations of text similarity in full text biomedical publications","volume":"5","author":"Sun","year":"2010","journal-title":"PloS ONE"},{"key":"2016122618203570000_2016.0.baw161.50","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks563"},{"key":"2016122618203570000_2016.0.baw161.51","unstructured":"Caporaso J.G. Deshpande N. Fink J.L. . (2008) Intrinsic evaluation of text mining tools may not predict performance on realistic tasks. Pac Symp Biocomput, 640\u2013651."},{"key":"2016122618203570000_2016.0.baw161.52","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-492"},{"key":"2016122618203570000_2016.0.baw161.53","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv024"},{"key":"2016122618203570000_2016.0.baw161.54","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340230303"},{"key":"2016122618203570000_2016.0.baw161.55","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/prot.24452","article-title":"Critical assessment of methods of protein structure prediction (CASP)\u2013round x","volume":"82","author":"Moult","year":"2014","journal-title":"Proteins"},{"key":"2016122618203570000_2016.0.baw161.56","doi-asserted-by":"crossref","unstructured":"Mao Y. Van Auken K. Li D. . (2014) Overview of the gene ontology task at BioCreative IV. Database (Oxford), 2014, bau086.","DOI":"10.1093\/database\/bau086"},{"key":"2016122618203570000_2016.0.baw161.57","doi-asserted-by":"publisher","DOI":"10.1136\/amiajnl-2010-000055"},{"key":"2016122618203570000_2016.0.baw161.58","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-S9-S2"},{"key":"2016122618203570000_2016.0.baw161.59","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-s1-s3"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/2016\/0\/baw161\/8658278\/baw161.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,15]],"date-time":"2019-09-15T12:59:35Z","timestamp":1568552375000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article-lookup\/doi\/10.1093\/database\/baw161"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"references-count":59,"alternative-id":["10.1093\/database\/baw161"],"URL":"https:\/\/doi.org\/10.1093\/database\/baw161","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016]]}}}