{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T12:18:02Z","timestamp":1779365882479,"version":"3.53.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,1,16]],"date-time":"2013-01-16T00:00:00Z","timestamp":1358294400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1471-2105-14-2","type":"journal-article","created":{"date-parts":[[2013,1,16]],"date-time":"2013-01-16T11:19:58Z","timestamp":1358335198000},"source":"Crossref","is-referenced-by-count":45,"title":["BioCause: Annotating and analysing causality in the biomedical domain"],"prefix":"10.1186","volume":"14","author":[{"given":"Claudiu","family":"Mih\u0103il\u0103","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomoko","family":"Ohta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sampo","family":"Pyysalo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophia","family":"Ananiadou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,1,16]]},"reference":[{"key":"5765_CR1","volume-title":"Text Mining for Biology And Biomedicine","author":"S Ananiadou","year":"2006","unstructured":"Ananiadou S, McNaught J(eds): Text Mining for Biology And Biomedicine. 2006, Boston, MA, USA: Artech House, Inc., [ http:\/\/www.artechhouse.com\/Detail.aspx?strBookId=1180 ]"},{"key":"5765_CR2","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1093\/bib\/6.1.57","volume":"6","author":"AM Cohen","year":"2005","unstructured":"Cohen AM, Hersh WR: A survey of current work in biomedical text mining. Briefings in Bioinf. 2005, 6: 57-71. [ http:\/\/bib.oxfordjournals.org\/content\/6\/1\/57.abstract ]","journal-title":"Briefings in Bioinf"},{"issue":"12","key":"5765_CR3","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1016\/j.tibtech.2006.10.002","volume":"24","author":"S Ananiadou","year":"2006","unstructured":"Ananiadou S, Kell DB, Tsujii J: Text mining and its potential applications in systems biology. Trends in Biotechnol. 2006, 24 (12): 571-579.","journal-title":"Trends in Biotechnol"},{"key":"5765_CR4","doi-asserted-by":"publisher","first-page":"e20","DOI":"10.1371\/journal.pcbi.0040020","volume":"4","author":"KB Cohen","year":"2008","unstructured":"Cohen KB, Hunter L: Getting Started in Text Mining. PLoS Comput Biol. 2008, 4: e20-[ http:\/\/dx.plos.org\/10.1371 ]","journal-title":"PLoS Comput Biol"},{"key":"5765_CR5","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.jbi.2003.10.001","volume":"37","author":"A Rzhetsky","year":"2004","unstructured":"Rzhetsky A, Iossifov I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Dubou\u00e9 AP, Weng W, Wilbur W, Hatzivassiloglou V, Friedman C: GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inf. 2004, 37: 43-53. [ http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1532046403001126 ]","journal-title":"J Biomed Inf"},{"key":"5765_CR6","first-page":"1017","volume-title":"Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics","author":"Y Miyao","year":"2006","unstructured":"Miyao Y, Ohta T, Masuda K, Tsuruoka Y, Yoshida K, Ninomiya T, Tsujii J: Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics. 2006, Sydney, Australia, 1017-1024."},{"issue":"5","key":"5765_CR7","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1093\/bib\/bbm045","volume":"8","author":"P Zweigenbaum","year":"2007","unstructured":"Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB: Frontiers of biomedical text mining: current progress. Briefings in Bioinformatics. 2007, 8 (5): 358-375.","journal-title":"Briefings in Bioinformatics"},{"key":"5765_CR8","first-page":"707","volume-title":"Proceedings of the Pacific Symposium on Biocomputing","author":"K Fukuda","year":"1998","unstructured":"Fukuda K, Tsunoda T, Tamura A, Takagi T: Toward Information Extraction: Identifying protein names from biological papers. Proceedings of the Pacific Symposium on Biocomputing. 1998, Hawaii, USA, 707-718."},{"key":"5765_CR9","first-page":"83","volume-title":"Proceedings of BioNLP 2011 Workshop","author":"RTB Batista-Navarro","year":"2011","unstructured":"Batista-Navarro RTB, Ananiadou S: Building a coreference-annotated corpus from the domain of biochemistry. Proceedings of BioNLP 2011 Workshop. 2011, Portland, OR, USA, 83-91. [ http:\/\/aclweb.org\/anthology-new\/W\/W11\/W11-0210.pdf ]"},{"issue":"4","key":"5765_CR10","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1136\/amiajnl-2011-000108","volume":"18","author":"GK Savova","year":"2011","unstructured":"Savova GK, Chapman WW, Zheng J, Crowley RS: Anaphoric relations in the clinical narrative: corpus creation. J Am Med Inf Assoc. 2011, 18 (4): 459-465. [ http:\/\/jamia.bmj.com\/content\/18\/4\/459.abstract ]","journal-title":"J Am Med Inf Assoc"},{"issue":"12","key":"5765_CR11","doi-asserted-by":"publisher","first-page":"e39","DOI":"10.1016\/j.ijmedinf.2009.04.010","volume":"78","author":"M Miwa","year":"2009","unstructured":"Miwa M, S\u00e6tre R, Miyao Y, Tsujii J: Protein-Protein Interaction Extraction by Leveraging Multiple Kernels and Parsers. Int J Med Inf. 2009, 78 (12): e39-e46.","journal-title":"Int J Med Inf"},{"key":"5765_CR12","first-page":"1","volume-title":"Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing","author":"S Pyysalo","year":"2009","unstructured":"Pyysalo S, Ohta T, Kim JD, Tsujii J: Static relations: a piece in the biomedical information extraction puzzle. Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing. 2009, BioNLP \u201909, Stroudsburg, PA, USA: Association for Computational Linguistics, 1-9."},{"key":"5765_CR13","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1142\/S0219720010004586","volume":"8","author":"M Miwa","year":"2010","unstructured":"Miwa M, S\u00e6tre R, Kim JD, Tsujii J: Event Extraction with Complex Event Classification Using Rich Features. J Bioinf Comput Biol. 2010, 8: 131-146.","journal-title":"J Bioinf Comput Biol"},{"key":"5765_CR14","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/1471-2105-13-108","volume":"13","author":"M Miwa","year":"2012","unstructured":"Miwa M, Thompson P, McNaught J, Kell DB, Ananiadou S: Extracting semantically enriched events from biomedical literature. BMC Bioinformatics. 2012, 13: 108-[ http:\/\/www.biomedcentral.com\/1471-2105\/13\/108\/ ]","journal-title":"BMC Bioinformatics"},{"issue":"13","key":"5765_CR15","doi-asserted-by":"publisher","first-page":"1759","DOI":"10.1093\/bioinformatics\/bts237","volume":"28","author":"M Miwa","year":"2012","unstructured":"Miwa M, Thompson P, Ananiadou S: Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. Bioinformatics. 2012, 28 (13): 1759-1765. [ http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/bts237?ijkey=oTLQoB9dzQDyjzV%26keytype=ref ]","journal-title":"Bioinformatics"},{"issue":"4","key":"5765_CR16","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1111\/j.1467-8640.2011.00398.x","volume":"27","author":"JD Kim","year":"2011","unstructured":"Kim JD, Ohta T, Pyysalo S, Kano Y, Tsujii J: Extracting Bio-Molecular Events From Literature-The BioNLP\u201909 Shared Task. Comput Intell. 2011, 27 (4): 513-540. 10.1111\/j.1467-8640.2011.00398.x\/abstract.","journal-title":"Comput Intell"},{"key":"5765_CR17","first-page":"1","volume-title":"Proceedings of the BioNLP Shared Task 2011 Workshop","author":"JD Kim","year":"2011","unstructured":"Kim JD, Pyysalo S, Ohta T, Bossy R, Nguyen N, Tsujii J: Overview of BioNLP Shared Task 2011. Proceedings of the BioNLP Shared Task 2011 Workshop. 2011, Portland, Oregon, USA: Association for Computational Linguistics, 1-6. [ http:\/\/www.aclweb.org\/anthology\/W11-1801 ]"},{"issue":"6","key":"5765_CR18","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.ipm.2007.01.018","volume":"43","author":"X Ling","year":"2007","unstructured":"Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B: Generating gene summaries from biomedical literature: A study of semi-structured summarization. Inf Process & Manage. 2007, 43 (6): 1777-1791. [ http:\/\/www.sciencedirect.com\/science\/article\/pii\/S030645730700043X ]","journal-title":"Inf Process & Manage"},{"issue":"8","key":"5765_CR19","doi-asserted-by":"publisher","first-page":"e23862","DOI":"10.1371\/journal.pone.0023862","volume":"6","author":"Y Shang","year":"2011","unstructured":"Shang Y, Li Y, Lin H, Yang Z: Enhancing Biomedical Text Summarization Using Semantic Relation Extraction. PLoS ONE. 2011, 6 (8): e23862-","journal-title":"PLoS ONE"},{"issue":"3","key":"5765_CR20","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.jbi.2007.03.002","volume":"40","author":"H Yu","year":"2007","unstructured":"Yu H, Lee M, Kaufman D, Ely J, Osheroff JA, Hripcsak G, Cimino J: Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. J Biomed Inf. 2007, 40 (3): 236-251. [ http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1532046407000202 ]","journal-title":"J Biomed Inf"},{"key":"5765_CR21","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1145\/2110363.2110372","volume-title":"Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium","author":"AB Abacha","year":"2012","unstructured":"Abacha AB, Zweigenbaum P: Medical question answering: translating medical questions into sparql queries. Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium. 2012, Miami, FL, USA, 41-50."},{"issue":"14","key":"5765_CR22","doi-asserted-by":"publisher","first-page":"e446","DOI":"10.1093\/bioinformatics\/btl235","volume":"22","author":"H Shatkay","year":"2006","unstructured":"Shatkay H, Chen N, Blostein D: Integrating image data into biomedical text categorization. Bioinformatics. 2006, 22 (14): e446-e453. [ http:\/\/bioinformatics.oxfordjournals.org\/content\/22\/14\/e446.abstract ]","journal-title":"Bioinformatics"},{"key":"5765_CR23","doi-asserted-by":"crossref","unstructured":"Kontonatsios G, Korkontzelos I, Ananiadou S: Developing Multilingual Text Mining Workflows in UIMA and U-Compare. Proceedings of the 17th International conference on Applications of Natural Language Processing to Information Systems. Groningen, Netherlands, 2012-2012.","DOI":"10.1007\/978-3-642-31178-9_8"},{"key":"5765_CR24","first-page":"1148","volume-title":"Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012)","author":"X Wang","year":"2012","unstructured":"Wang X, Thompson P, Ananiadou S: Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries. Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012). 2012, Istanbul, Turkey, 1148-1155. [ http:\/\/www.lrec-conf.org\/proceedings\/lrec2012\/pdf\/316_Paper.pdf ]"},{"issue":"15","key":"5765_CR25","doi-asserted-by":"publisher","first-page":"1997","DOI":"10.1093\/bioinformatics\/btp289","volume":"25","author":"Y Kano","year":"2009","unstructured":"Kano Y, Baumgartner W, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J: U-Compare: share and compare text mining tools with UIMA. Bioinformatics. 2009, 25 (15): 1997-1998.","journal-title":"Bioinformatics"},{"key":"5765_CR26","volume-title":"Database: J Biol Databases and Curation","author":"R Rak","year":"2012,","unstructured":"Rak R, Rowley A, Black W, Ananiadou S: Argo: an integrative, interactive, text mining-based workbench supporting curation. Database: J Biol Databases and Curation. 2012,, 2012. [ http:\/\/database.oxfordjournals.org\/content\/2012\/bas010.full?keytype=ref%26ijkey=i0zkIYyxcsdxhfN ]"},{"key":"5765_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-7-356","volume":"7","author":"W Wilbur","year":"2006","unstructured":"Wilbur W, Rzhetsky A, Shatkay H: New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinformatics. 2006, 7: 1-10. 10.1186\/1471-2105-7-356.","journal-title":"BMC Bioinformatics"},{"key":"5765_CR28","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1186\/1471-2105-12-393","volume":"12","author":"P Thompson","year":"2011","unstructured":"Thompson P, Nawaz R, McNaught J, Ananiadou S: Enriching a biomedical event corpus with meta-knowledge annotation. BMC Bioinformatics. 2011, 12: 393-[ http:\/\/www.biomedcentral.com\/1471-2105\/12\/393 ]","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 11","key":"5765_CR29","doi-asserted-by":"publisher","first-page":"S10","DOI":"10.1186\/1471-2105-9-S11-S10","volume":"9","author":"H Kilicoglu","year":"2008","unstructured":"Kilicoglu H, Bergler S: Recognizing speculative language in biomedical research articles: a linguistically motivated perspective. BMC Bioinformatics. 2008, 9 (Suppl 11): S10-[ http:\/\/www.biomedcentral.com\/1471-2105\/9\/S11\/S10 ]","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"5765_CR30","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1016\/j.jbi.2010.08.003","volume":"43","author":"S Agarwal","year":"2010","unstructured":"Agarwal S, Yu H: Detecting hedge cues and their scope in biomedical text with conditional random fields. J Biomed Inf. 2010, 43 (6): 953-961.","journal-title":"J Biomed Inf"},{"issue":"Suppl 11","key":"5765_CR31","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1186\/1471-2105-9-S11-S9","volume":"9","author":"V Vincze","year":"2008","unstructured":"Vincze V, Szarvas G, Farkas R, Mora G, Csirik J: The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes. BMC Bioinformatics. 2008, 9 (Suppl 11): S9-","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"5765_CR32","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1162\/COLI_a_00095","volume":"38","author":"R Morante","year":"2012","unstructured":"Morante R, Sporleder C: Modality and Negation: An Introduction to the Special Issue. Comput Linguistics. 2012, 38 (2): 223-260. 10.1162\/COLI_a_00095.","journal-title":"Comput Linguistics"},{"issue":"6","key":"5765_CR33","first-page":"696","volume":"17","author":"S Agarwal","year":"2010","unstructured":"Agarwal S, Yu H: Biomedical negation scope detection with conditional random fields. JAMIA. 2010, 17 (6): 696-701.","journal-title":"JAMIA"},{"key":"5765_CR34","first-page":"3505","volume-title":"Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012)","author":"R Nawaz","year":"2012","unstructured":"Nawaz R, Thompson P, Ananiadou S: Identification of Manner in Bio-Events. Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012). 2012, Istanbul, Turkey, 3505-3510. [ http:\/\/www.lrec-conf.org\/proceedings\/lrec2012\/pdf\/818_Paper.pdf ]"},{"key":"5765_CR35","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1186\/1471-2105-11-492","volume":"11","author":"KB Cohen","year":"2010","unstructured":"Cohen KB, Johnson H, Verspoor K, Roeder C, Hunter L: The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics. 2010, 11: 492-","journal-title":"BMC Bioinformatics"},{"key":"5765_CR36","first-page":"24","volume-title":"Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012)","author":"R Nawaz","year":"2012","unstructured":"Nawaz R, Thompson P, Ananiadou S: Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers. In. Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012). 2012, Istanbul, Turkey: European Language Resources Association, 24-31. [ http:\/\/www.nactem.ac.uk\/papers\/Nawaz_BioTxtM_2012.pdf ]"},{"issue":"23","key":"5765_CR37","doi-asserted-by":"publisher","first-page":"3174","DOI":"10.1093\/bioinformatics\/btp548","volume":"25","author":"S Agarwal","year":"2009","unstructured":"Agarwal S, Yu H: Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion. Bioinformatics. 2009, 25 (23): 3174-3180.","journal-title":"Bioinformatics"},{"key":"5765_CR38","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2105-9-10","volume":"9","author":"JD Kim","year":"2008","unstructured":"Kim JD, Ohta T, Tsujii J: Corpus annotation for mining biomedical events from literature. BMC Bioinformatics. 2008, 9: 10-","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"5765_CR39","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/1471-2105-6-S1-S3","volume":"6","author":"L Tanabe","year":"2005","unstructured":"Tanabe L, Xie N, Thom L, Matten W, Wilbur WJ: GENETAG: a tagged corpus for gene\/protein named entity recognition. BMC Bioinformatics. 2005, 6 (Suppl 1): S3-","journal-title":"BMC Bioinformatics"},{"key":"5765_CR40","doi-asserted-by":"publisher","first-page":"76","DOI":"10.3115\/1119312.1119322","volume-title":"Proceedings of the ACL 2003 workshop on Multilingual summarization and question answering - Volume 12","author":"R Girju","year":"2003","unstructured":"Girju R: Automatic detection of causal relations for Question Answering. Proceedings of the ACL 2003 workshop on Multilingual summarization and question answering - Volume 12. 2003, MultiSumQA \u201903, Stroudsburg, PA, USA: Association for Computational Linguistics, 76-83."},{"key":"5765_CR41","first-page":"310","volume-title":"Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC\u201908)","author":"E Blanco","year":"2008","unstructured":"Blanco E, Castell N, Moldovan D: Causal Relation Extraction. Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC\u201908). Edited by: Calzolari N, Choukri K, Maegaard B, Mariani J, Odjik J, Piperidis S, Tapias D. 2008, Marrakech, Morocco: European Language Resources Association (ELRA), 310-313."},{"key":"5765_CR42","first-page":"177","volume-title":"Advances in Soft Computing, Volume 6438 of Lecture Notes in Computer Science","author":"MA R\u00edos Gaona","year":"2010","unstructured":"R\u00edos Gaona, M A, Gelbukh A, Bandyopadhyay S: Recognizing Textual Entailment Using a Machine Learning Approach. Advances in Soft Computing, Volume 6438 of Lecture Notes in Computer Science. Edited by: Sidorov G, Hern\u00e1ndez Aguirre A, Reyes Garc\u00eda C. 2010, Germany, Berlin: Springer Berlin \/ Heidelberg, 177-185."},{"key":"5765_CR43","first-page":"2626","volume-title":"Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC\u201910)","author":"C Grivaz","year":"2010","unstructured":"Grivaz C: Human Judgements on Causation in French Texts. Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC\u201910). Edited by: Calzolari N, Choukri K, Maegaard B, Mariani J, Odijk J, Piperidis S, Rosner M, Tapias D. 2010, Valetta, Malta: European Language Resources Association, 2626-2631."},{"key":"5765_CR44","first-page":"908","volume-title":"Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC\u201908)","author":"S Bethard","year":"2008","unstructured":"Bethard S, Corvey W, Klingenstein S, Martin JH: Building a Corpus of Temporal-Causal Structure. Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC\u201908). Edited by: Calzolari N, Choukri K, Maegaard B, Mariani J, Odijk J, Piperidis S, Tapias D. 2008, Marrakech, Morocco: European Language Resources Association, 908-915."},{"issue":"6","key":"5765_CR45","doi-asserted-by":"publisher","first-page":"1102","DOI":"10.1016\/j.jbi.2011.07.001","volume":"44","author":"S Kleinberg","year":"2011","unstructured":"Kleinberg S, Hripcsak G: A review of causal inference for biomedical informatics. J Biomed Inf. 2011, 44 (6): 1102-1112. [ http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1532046411001195 ]","journal-title":"J Biomed Inf"},{"key":"5765_CR46","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/1471-2105-8-50","volume":"8","author":"S Pyysalo","year":"2007","unstructured":"Pyysalo S, Ginter F, Heimonen J, Bjorne J, Boberg J, Jarvinen J, Salakoski T: BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinformatics. 2007, 8: 50-","journal-title":"BMC Bioinformatics"},{"key":"5765_CR47","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1186\/1471-2105-10-349","volume":"10","author":"P Thompson","year":"2009","unstructured":"Thompson P, Iqbal S, McNaught J, Ananiadou S: Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics. 2009, 10: 349-","journal-title":"BMC Bioinformatics"},{"key":"5765_CR48","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. Nat Genet. 2000, 25: 25-29.","journal-title":"Nat Genet"},{"issue":"suppl 1","key":"5765_CR49","first-page":"D262\u2014266","volume":"32","author":"E Camon","year":"2004","unstructured":"Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R: The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucl Acids Res. 2004, 32 (suppl 1): D262\u2014266-[ http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/32\/suppl_1\/D262 ]","journal-title":"Nucl Acids Res"},{"issue":"12","key":"5765_CR50","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/nrg3096","volume":"12","author":"S Ghosh","year":"2011","unstructured":"Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H: Software for systems biology: from tools to integrated platforms. Nat Rev Genet. 2011, 12 (12): 821-832.","journal-title":"Nat Rev Genet"},{"issue":"4","key":"5765_CR51","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19 (4): 524-531.","journal-title":"Bioinformatics"},{"issue":"8","key":"5765_CR52","doi-asserted-by":"publisher","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","volume":"96","author":"A Funahashi","year":"2008","unstructured":"Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H: CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proc IEEE. 2008, 96 (8): 1254-1265.","journal-title":"Proc IEEE"},{"key":"5765_CR53","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1007\/978-1-60761-175-2_7","volume":"563","author":"H Mi","year":"2009","unstructured":"Mi H, Thomas P: PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009, 563: 123-140.","journal-title":"Methods Mol Biol"},{"key":"5765_CR54","first-page":"105","volume-title":"Proceedings of BioNLP 2011 Workshop","author":"T Ohta","year":"2011","unstructured":"Ohta T, Pyysalo S, Tsujii J: From Pathways to Biomolecular Events: Opportunities and Challenges. Proceedings of BioNLP 2011 Workshop. 2011, Portland, Oregon, USA: Association for Computational Linguistics, 105-113."},{"key":"5765_CR55","first-page":"16","volume-title":"Proceedings of BioNLP Shared Task 2011 Workshop","author":"T Ohta","year":"2011","unstructured":"Ohta T, Pyysalo S, Tsujii J: Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. Proceedings of BioNLP Shared Task 2011 Workshop. 2011, Stroudsburg, PA, USA: Association for Computational Linguistics, 16-25."},{"key":"5765_CR56","first-page":"26","volume-title":"Proceedings of the BioNLP Shared Task 2011 Workshop","author":"S Pyysalo","year":"2011","unstructured":"Pyysalo S, Ohta T, Rak R, Sullivan D, Mao C, Wang C, Sobral B, Tsujii J, Ananiadou S: Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. Proceedings of the BioNLP Shared Task 2011 Workshop. 2011, Portland, Oregon, USA: Association for Computational Linguistics, 26-35. [ http:\/\/www.aclweb.org\/anthology\/W11-1804 ]"},{"key":"5765_CR57","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1186\/1471-2105-12-188","volume":"12","author":"R Prasad","year":"2011","unstructured":"Prasad R, McRoy S, Frid N, Joshi A, Yu H: The Biomedical Discourse Relation Bank. BMC Bioinformatics. 2011, 12: 188-","journal-title":"BMC Bioinformatics"},{"key":"5765_CR58","first-page":"2961","volume-title":"In Proceedings of the 6th International Conference on language Resources and Evaluation (LREC)","author":"R Prasad","year":"2008","unstructured":"Prasad R, Dinesh N, Lee A, Miltsakaki E, Robaldo L, Joshi A, Webber B: The Penn Discourse TreeBank 2.0. In Proceedings of the 6th International Conference on language Resources and Evaluation (LREC). Edited by: Calzolari N, Choukri K, Maegaard B, Mariani J, Odijk J, Piperidis S, Tapias D. 2008, Marrakech, Morocco, 2961-2968."},{"key":"5765_CR59","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1186\/1471-2105-12-212","volume":"12","author":"T Lippincott","year":"2011","unstructured":"Lippincott T, Seaghdha D, Korhonen A: Exploring subdomain variation in biomedical language. BMC Bioinformatics. 2011, 12: 212-","journal-title":"BMC Bioinformatics"},{"key":"5765_CR60","first-page":"38","volume-title":"EACL","author":"C Mih\u0103il\u0103","year":"2012","unstructured":"Mih\u0103il\u0103 C, Batista-Navarro RT: What\u2019s in a Name? Entity Type Variation across Two Biomedical Subdomains. EACL. Edited by: Daelemans W, Lapata M. 2012, M\u00e0rquez L. The Association for Computer Linguistics: Avignon, France, 38-45."},{"key":"5765_CR61","first-page":"1","volume-title":"Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012)","author":"C Mih\u0103il\u0103","year":"2012","unstructured":"Mih\u0103il\u0103 C, Batista-Navarro RT, Ananiadou S: Analysing Entity Type Variation across Biomedical Subdomains. Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012). Edited by: Ananiadou S, Cohen K, Demner-Fushman D, Thompson P. 2012, Istanbul, Turkey, 1-7."},{"issue":"16","key":"5765_CR62","doi-asserted-by":"publisher","first-page":"2597","DOI":"10.1093\/bioinformatics\/bth291","volume":"20","author":"MJ Schuemie","year":"2004","unstructured":"Schuemie MJ, Weeber M, Schijvenaars BJA, van Mulligen, van der Eijk, Jelier R, Mons B, Kors JA: Distribution of information in biomedical abstracts and full-text publications. Bioinformatics. 2004, 20 (16): 2597-2604. [ http:\/\/bioinformatics.oxfordjournals.org\/content\/20\/16\/2597.abstract ]","journal-title":"Bioinformatics"},{"key":"5765_CR63","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/1471-2105-4-20","volume":"4","author":"P Shah","year":"2003","unstructured":"Shah P, Perez-Iratxeta C, Bork P, Andrade M: Information extraction from full text scientific articles: Where are the keywords?. BMC Bioinformatics. 2003, 4: 20-[ http:\/\/www.biomedcentral.com\/1471-2105\/4\/20 ]","journal-title":"BMC Bioinformatics"},{"key":"5765_CR64","first-page":"102","volume-title":"Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics. Association for Computational Linguistics","author":"P Stenetorp","year":"2012","unstructured":"Stenetorp P, Pyysalo S, Topi\u0107 G, Ohta T, Ananiadou S, Tsujii J: brat: a Web-based Tool for NLP-Assisted Text Annotation. Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics. Association for Computational Linguistics. 2012, Avignon, France, 102-107. [ http:\/\/aclweb.org\/anthology-new\/E\/E12\/E12-2021.pdf ]"},{"key":"5765_CR65","volume-title":"Statistical Methods for Rates and Proportions","author":"JL Fleiss","year":"1981","unstructured":"Fleiss JL: Statistical Methods for Rates and Proportions. 1981, New York: John Wiley & Sons"},{"issue":"3","key":"5765_CR66","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1197\/jamia.M1733","volume":"12","author":"G Hripcsak","year":"2005","unstructured":"Hripcsak G, Rothschild AS: Agreement, the F-Measure, and Reliability in Information Retrieval. J Am Med Inf Assoc. 2005, 12 (3): 296-298. [ http:\/\/jamia.bmj.com\/content\/12\/3\/296.abstract ]","journal-title":"J Am Med Inf Assoc"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,8]],"date-time":"2019-07-08T10:39:26Z","timestamp":1562582366000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,16]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["5765"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1,16]]},"article-number":"2"}}