{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T19:49:57Z","timestamp":1768679397060,"version":"3.49.0"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2015,9,25]],"date-time":"2015-09-25T00:00:00Z","timestamp":1443139200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004391","type":"journal-article","created":{"date-parts":[[2015,9,25]],"date-time":"2015-09-25T18:33:31Z","timestamp":1443206011000},"page":"e1004391","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":50,"title":["miRTex: A Text Mining System for miRNA-Gene Relation Extraction"],"prefix":"10.1371","volume":"11","author":[{"given":"Gang","family":"Li","sequence":"first","affiliation":[]},{"given":"Karen E.","family":"Ross","sequence":"additional","affiliation":[]},{"given":"Cecilia N.","family":"Arighi","sequence":"additional","affiliation":[]},{"given":"Yifan","family":"Peng","sequence":"additional","affiliation":[]},{"given":"Cathy H.","family":"Wu","sequence":"additional","affiliation":[]},{"given":"K.","family":"Vijay-Shanker","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2015,9,25]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/0092-8674(93)90529-Y","article-title":"The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14","volume":"75","author":"RC Lee","year":"1993","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1146\/annurev-biochem-060308-103103","article-title":"Regulation of mRNA translation and stability by microRNAs","volume":"79","author":"MR Fabian","year":"2010","journal-title":"Annu Rev Biochem"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"478","DOI":"10.2174\/138920209789208219","article-title":"Survey of Computational Algorithms for MicroRNA Target Prediction","volume":"10","author":"D Yue","year":"2009","journal-title":"Curr Genomics"},{"key":"ref4","article-title":"MicroRNAs\u2013targeting and target prediction","author":"T Saito","year":"2010","journal-title":"N Biotechnol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"93","DOI":"10.2174\/156652411794859250","article-title":"Practical Aspects of microRNA Target Prediction","volume":"11","author":"TM Witkos","year":"2011","journal-title":"Curr Mol Med"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/978-1-62703-748-8_12","article-title":"Computational methods for microRNA target prediction","volume":"1107","author":"H Hamzeiy","year":"2014","journal-title":"Methods Mol Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.ymeth.2007.09.005","article-title":"Experimental validation of miRNA targets","volume":"44","author":"DE Kuhn","year":"2008","journal-title":"Methods"},{"issue":"Suppl 8","key":"ref8","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2105-12-S8-S1","article-title":"Overview of the BioCreative III Workshop","volume":"12","author":"CN Arighi","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref9","unstructured":"Kim JD, Wang Y, Yasunori Y (2013) The Genia Event Extraction Shared Task, 2013 Edition-Overview. ACL 2013. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.aclweb.org\/anthology\/W\/W13\/W13-20.pdf#page=20\" xlink:type=\"simple\">http:\/\/www.aclweb.org\/anthology\/W\/W13\/W13-20.pdf#page=20<\/ext-link>."},{"key":"ref10","unstructured":"Segura-Bedmar I, Mart\u0131nez P, Herrero-Zazo M. Semeval-2013 task 9: Extraction of drug-drug interactions from biomedical texts (ddiextraction 2013). Proceedings of Semeval. 2013; 341\u2013350."},{"key":"ref11","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/1471-2105-11-135","article-title":"miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature","volume":"11","author":"H Naeem","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1197\/jamia.M2401","article-title":"Automated acquisition of disease drug knowledge from biomedical and clinical documents: an initial study","volume":"15","author":"ES Chen","year":"2008","journal-title":"J Am Med Inform Assoc"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1093\/bioinformatics\/btq667","article-title":"Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature","volume":"27","author":"E Doughty","year":"2011","journal-title":"Bioinformatics"},{"key":"ref14","unstructured":"Torii M, Arighi CN, Li G, Wang Q, Wu CH, Vijay-Shanker K. (2014) RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE\/ACM Trans Comput Biol Bioinform PP: 1\u20131."},{"key":"ref15","doi-asserted-by":"crossref","DOI":"10.1093\/database\/bav020","article-title":"Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system","volume":"2015","author":"CO Tudor","year":"2015","journal-title":"Database"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1186\/1471-2105-15-285","article-title":"A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems","volume":"15","author":"Y Peng","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"ref17","unstructured":"Bui Q-C, Van Mulligen EM, Campos D, Kors JA. A fast rule-based approach for biomedical event extraction. Proceedings of the BioNLP Shared Task 2013 Workshop. 2013. pp. 104\u2013108."},{"key":"ref18","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511801389","article-title":"An introduction to support vector machines and other kernel-based learning methods","author":"N Cristianini","year":"2000"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1371\/journal.pcbi.0030129","article-title":"A primer on learning in Bayesian networks for computational biology","volume":"3","author":"CJ Needham","year":"2007","journal-title":"PLoS Comput Biol"},{"issue":"Suppl 11","key":"ref20","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-9-S11-S2","article-title":"All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning","volume":"9","author":"A Airola","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.1016\/j.ijmedinf.2009.04.010","article-title":"Protein-protein interaction extraction by leveraging multiple kernels and parsers","volume":"78","author":"M Miwa","year":"2009","journal-title":"Int J Med Inform"},{"key":"ref22","doi-asserted-by":"crossref","unstructured":"Peng Y, Tudor CO, Torii M, Wu CH, Vijay-Shanker K (2012) iSimp: A sentence simplification system for biomedical text. Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on. pp. 1\u20136.","DOI":"10.1109\/BIBM.2012.6392671"},{"key":"ref23","doi-asserted-by":"crossref","unstructured":"Bagewadi S, Bobi\u0107 T, Hofmann-Apitius M, Fluck J, Klinger R (2014) Detecting miRNA Mentions and Relations in Biomedical Literature. F1000Res 3. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/dx.doi.org\/10.12688\/f1000research.4591.1\" xlink:type=\"simple\">http:\/\/dx.doi.org\/10.12688\/f1000research.4591.1<\/ext-link>.","DOI":"10.12688\/f1000research.4591.1"},{"key":"ref24","first-page":"1871","article-title":"LIBLINEAR: A Library for Large Linear Classification","volume":"9","author":"R-E Fan","year":"2008","journal-title":"J Mach Learn Res. JMLR.org"},{"key":"ref25","first-page":"27:1","article-title":"ACM Trans Intell Syst Technol","volume":"2","author":"C-C Chang","year":"2011"},{"key":"ref26","article-title":"DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions","author":"IS Vlachos","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/978-1-4939-1062-5_25","article-title":"miRWalk database for miRNA-target interactions","volume":"1182","author":"H Dweep","year":"2014","journal-title":"Methods Mol Biol"},{"key":"ref28","article-title":"miRTarBase: a database curates experimentally validated microRNA\u2013target interactions","author":"S-D Hsu","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"D78","DOI":"10.1093\/nar\/gkt1266","article-title":"miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions","volume":"42","author":"S-D Hsu","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"D105","DOI":"10.1093\/nar\/gkn851","article-title":"miRecords: an integrated resource for microRNA\u2013target interactions","volume":"37","author":"F Xiao","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1261\/rna.965408","article-title":"miRDB: a microRNA target prediction and functional annotation database with a wiki interface","volume":"14","author":"X Wang","year":"2008","journal-title":"RNA"},{"key":"ref32","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1209s29","article-title":"miRBase: microRNA sequences and annotation","author":"S Griffiths-Jones","year":"2010","journal-title":"Curr Protoc Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"D98","DOI":"10.1093\/nar\/gkn714","article-title":"miR2Disease: a manually curated database for microRNA deregulation in human disease","volume":"37","author":"Q Jiang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","article-title":"Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data","volume":"43","author":"WA Kibbe","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1097\/PPO.0b013e3181d3eef5","article-title":"Triple-negative breast cancers: a view from 10,000 feet","volume":"16","author":"M Ray","year":"2010","journal-title":"Cancer J"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1093\/jxb\/ert353","article-title":"Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana","volume":"65","author":"MY Xu","year":"2014","journal-title":"J Exp Bot"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1111\/j.1365-313X.2006.02980.x","article-title":"ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination","volume":"49","author":"JL Reyes","year":"2007","journal-title":"Plant J"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"e57547","DOI":"10.1371\/journal.pone.0057547","article-title":"Tight interconnection and multi-level control of Arabidopsis MYB44 in MAPK cascade signalling","volume":"8","author":"H Persak","year":"2013","journal-title":"PLoS One"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1054","DOI":"10.1016\/j.bbrc.2012.12.039","article-title":"Phosphorylation of the zinc finger transcriptional regulator ZAT6 by MPK6 regulates Arabidopsis seed germination under salt and osmotic stress","volume":"430","author":"X-M Liu","year":"2013","journal-title":"Biochem Biophys Res Commun"},{"key":"ref40","doi-asserted-by":"crossref","unstructured":"Manning CD, Surdeanu M, Bauer J, Finkel J (n.d.) The Stanford CoreNLP Natural Language Processing Toolkit. surdeanu.info. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.surdeanu.info\/mihai\/papers\/acl2014-corenlp.pdf\" xlink:type=\"simple\">http:\/\/www.surdeanu.info\/mihai\/papers\/acl2014-corenlp.pdf<\/ext-link>.","DOI":"10.3115\/v1\/P14-5010"},{"key":"ref41","first-page":"652","article-title":"BANNER: an executable survey of advances in biomedical named entity recognition","author":"R Leaman","year":"2008","journal-title":"Pac Symp Biocomput"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkh023","article-title":"The microRNA Registry","volume":"32","author":"S Griffiths-Jones","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1261\/rna.2183803","article-title":"A uniform system for microRNA annotation","volume":"9","author":"V Ambros","year":"2003","journal-title":"RNA"},{"key":"ref44","unstructured":"Charniak E (2000) A Maximum-entropy-inspired Parser. Proceedings of the 1st North American Chapter of the Association for Computational Linguistics Conference. NAACL 2000. Stroudsburg, PA, USA: Association for Computational Linguistics. pp. 132\u2013139."},{"key":"ref45","article-title":"Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing","author":"D Mcclosky","year":"2010"},{"key":"ref46","unstructured":"Levy R, Andrew G (2006) Tregex and Tsurgeon: tools for querying and manipulating tree data structures. Proceedings of the fifth international conference on."},{"key":"ref47","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1186\/1471-2105-11-492","article-title":"The structural and content aspects of abstracts versus bodies of full text journal articles are different","volume":"11","author":"KB Cohen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1007\/s13277-013-0708-0","article-title":"Expression and regulatory function of miRNA-182 in triple-negative breast cancer cells through its targeting of profilin 1","volume":"34","author":"H Liu","year":"2013","journal-title":"Tumour Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"4536","DOI":"10.1073\/pnas.1402604111","article-title":"Protective role of miR-155 in breast cancer through RAD51 targeting impairs homologous recombination after irradiation","volume":"111","author":"P Gasparini","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/srep00264","article-title":"Transcriptomic landscape of breast cancers through mRNA sequencing","volume":"2","author":"J Eswaran","year":"2012","journal-title":"Sci Rep"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"ME Smoot","year":"2011","journal-title":"Bioinformatics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"D1176","DOI":"10.1093\/nar\/gks1081","article-title":"PhosPhAt goes kinases\u2014searchable protein kinase target information in the plant phosphorylation site database PhosPhAt","volume":"41","author":"M Zulawski","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref53","article-title":"STRING v9. 1: protein-protein interaction networks, with increased coverage and integration","author":"A Franceschini","year":"2013","journal-title":"Nucleic acids"},{"key":"ref54","unstructured":"Del\u00e9ger L, Ligozat A-L, Grouin C, Zweigenbaum P, N\u00e9v\u00e9ol A. Annotation of specialized corpora using a comprehensive entity and relation scheme. Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC), Reykjavik: ELRA. 2014. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.lrec-conf.org\/proceedings\/lrec2014\/pdf\/552_Paper.pdf\" xlink:type=\"simple\">http:\/\/www.lrec-conf.org\/proceedings\/lrec2014\/pdf\/552_Paper.pdf<\/ext-link>"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"D191","DOI":"10.1093\/nar\/gkt1140","article-title":"Activities at the Universal Protein Resource (UniProt)","volume":"42","year":"2014","journal-title":"Nucleic Acids Res"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004391","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,22]],"date-time":"2022-05-22T08:21:10Z","timestamp":1653207670000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004391"}},"subtitle":[],"editor":[{"given":"Andrey","family":"Rzhetsky","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2015,9,25]]},"references-count":55,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2015,9,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004391","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9,25]]}}}