{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T10:13:30Z","timestamp":1773656010412,"version":"3.50.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model, facilitated by the maturation of basic tools for biomedical text analysis and the availability of manually annotated resources. The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction. A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction.<\/jats:p>\n               <jats:p>Results: This study considers event-based IE at PubMed scale. We introduce a system combining publicly available, state-of-the-art methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed citations. We present the first evaluation of the generalization performance of event extraction systems to this scale and show that despite its computational complexity, event extraction from the entire PubMed is feasible. We further illustrate the value of the extraction approach through a number of analyses of the extracted information.<\/jats:p>\n               <jats:p>Availability: The event detection system and extracted data are open source licensed and available at http:\/\/bionlp.utu.fi\/.<\/jats:p>\n               <jats:p>Contact: \u00a0jari.bjorne@utu.fi<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq180","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i382-i390","source":"Crossref","is-referenced-by-count":74,"title":["Complex event extraction at PubMed scale"],"prefix":"10.1093","volume":"26","author":[{"given":"Jari","family":"Bj\u00f6rne","sequence":"first","affiliation":[{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"},{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filip","family":"Ginter","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sampo","family":"Pyysalo","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun'ichi","family":"Tsujii","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"},{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tapio","family":"Salakoski","sequence":"additional","affiliation":[{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"},{"name":"1 Department of Information Technology, University of Turku, Turku, Finland, 2 Turku Centre for Computer Science (TUCS), Turku, 3 Department of Computer Science, University of Tokyo, Tokyo, Japan and 4 National Centre for Text Mining, University of Manchester, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"issue":"Suppl. 11","key":"2023012508080763700_B1","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":"Airola","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508080763700_B2","article-title":"Scope expands for PubMed\u00ae and MEDLINE\u00ae","volume":"311","author":"Benton","year":"1999","journal-title":"NLM Technical Bulletin"},{"key":"2023012508080763700_B3","first-page":"10","article-title":"Extracting complex biological events with rich graph-based feature sets","volume-title":"Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task.","author":"Bj\u00f6rne","year":"2009"},{"key":"2023012508080763700_B4","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1016\/j.jbi.2009.09.001","article-title":"Current issues in biomedical text mining and natural language processing","volume":"42","author":"Chapman","year":"2009","journal-title":"J. Biomed. Inform."},{"key":"2023012508080763700_B5","doi-asserted-by":"crossref","first-page":"173","DOI":"10.3115\/1219840.1219862","article-title":"Coarse-to-fine n-best parsing and maxent discriminative reranking","volume-title":"Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05).","author":"Charniak","year":"2005"},{"issue":"Suppl. 2","key":"2023012508080763700_B6","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/gb-2008-9-s2-s5","article-title":"MINT and IntAct contribute to the second BioCreative challenge: serving the text-mining community with high quality molecular interaction data","volume":"9","author":"Chatr-aryamontri","year":"2008","journal-title":"Genome Biol."},{"key":"2023012508080763700_B7","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/1471-2105-5-147","article-title":"Content-rich biological network constructed by mining PubMed abstracts","volume":"5","author":"Chen","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012508080763700_B8","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/bioinformatics\/btp245","article-title":"Bayesian inference of protein-protein interactions from biological literature","volume":"25","author":"Chowdhary","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012508080763700_B9","first-page":"449","article-title":"Generating typed dependency parses from phrase structure parses","author":"de Marneffe","year":"2006","journal-title":"Proceedings of LREC-06"},{"key":"2023012508080763700_B10","article-title":"The Stanford typed dependencies representation","author":"de Marneffe","year":"2008","journal-title":"COLING Workshop on Cross-framework and Cross-domain Parser Evaluation"},{"key":"2023012508080763700_B11","article-title":"Stanford typed dependencies manual","volume-title":"Technical report","author":"de Marneffe","year":"2008"},{"key":"2023012508080763700_B12","doi-asserted-by":"crossref","first-page":"W783","DOI":"10.1093\/nar\/gki470","article-title":"GoPubMed: exploring PubMed with the Gene Ontology","volume":"33","author":"Doms","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012508080763700_B13","doi-asserted-by":"crossref","first-page":"11","DOI":"10.3115\/1621410.1621412","article-title":"Evaluating impact of re-training a lexical disambiguation model on domain adaptation of an HPSG parser","volume-title":"IWPT '07: Proceedings of the 10th International Conference on Parsing Technologies.","author":"Hara","year":"2007"},{"key":"2023012508080763700_B14","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0168-9525(02)00014-8","article-title":"Life cycles of successful genes","volume":"19","author":"Hoffmann","year":"2003","journal-title":"Trends Genet."},{"key":"2023012508080763700_B15","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1038\/ng0704-664","article-title":"A gene network for navigating the literature","volume":"36","author":"Hoffmann","year":"2004","journal-title":"Nat. Genet."},{"key":"2023012508080763700_B16","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1186\/1471-2105-10-233","article-title":"A realistic assessment of methods for extracting gene\/protein interactions from free text","volume":"10","author":"Kabiljo","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012508080763700_B17","first-page":"70","article-title":"Introduction to the bio-entity recognition task at JNLPBA","volume-title":"Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA)","author":"Kim","year":"2004"},{"key":"2023012508080763700_B18","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1471-2105-9-10","article-title":"Corpus annotation for mining biomedical events from literature","volume":"9","author":"Kim","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508080763700_B19","first-page":"1","article-title":"Overview of BioNLP'09 shared task on event extraction","volume-title":"Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task.","author":"Kim","year":"2009"},{"issue":"Suppl. 2","key":"2023012508080763700_B20","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s2-s4","article-title":"Overview of the protein-protein interaction annotation extraction task of BioCreative II","volume":"9","author":"Krallinger","year":"2008","journal-title":"Genome Biol."},{"key":"2023012508080763700_B21","first-page":"652","article-title":"BANNER: an executable survey of advances in biomedical named entity recognition","volume":"13","author":"Leaman","year":"2008","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012508080763700_B22","first-page":"58","article-title":"Parsing biomedical literature","volume-title":"Proceedings of the Second International Joint Conference on Natural Langage Processing (IJCNLP'05)","author":"Lease","year":"2005"},{"key":"2023012508080763700_B23","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1007\/11575832_18","article-title":"Lydia: a system for large-scale news analysis","volume":"3772","author":"Lloyd","year":"2005","journal-title":"12th Symposium of String Processing and Information Retrieval (SPIRE '05)"},{"key":"2023012508080763700_B24","article-title":"Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing\/","volume-title":"PhD Thesis","author":"McClosky","year":"2009"},{"key":"2023012508080763700_B25","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":"Miwa","year":"2009","journal-title":"Int. J. Med. Inform."},{"key":"2023012508080763700_B26","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1142\/S0219720010004586","article-title":"Event extraction with complex event classification using rich features","volume":"8","author":"Miwa","year":"2010","journal-title":"J. Bioinform. Comput. Biol."},{"key":"2023012508080763700_B27","first-page":"31","article-title":"Learning language in logic - genic interaction extraction challenge","volume-title":"Proceedings of the 4th Learning Language in Logic Workshop (LLL05)","author":"N\u00e9dellec","year":"2005"},{"key":"2023012508080763700_B28","doi-asserted-by":"crossref","first-page":"17","DOI":"10.3115\/1225403.1225408","article-title":"An intelligent search engine and GUI-based efficient MEDLINE search tool based on deep syntactic parsing","volume-title":"Proceedings of the COLING\/ACL 2006 Interactive Presentation Sessions","author":"Ohta","year":"2006"},{"key":"2023012508080763700_B29","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1145\/1516360.1516498","article-title":"High-performance information extraction with AliBaba","volume-title":"EDBT","author":"Palaga","year":"2009"},{"key":"2023012508080763700_B30","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-8-50","article-title":"BioInfer: a corpus for information extraction in the biomedical domain","volume":"8","author":"Pyysalo","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012508080763700_B31","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.jbi.2008.12.004","article-title":"Porting a lexicalized-grammar parser to the biomedical domain","volume":"42","author":"Rimell","year":"2009","journal-title":"J. Biomed. Inform."},{"key":"2023012508080763700_B32","first-page":"105","article-title":"Integrated network construction using event based text mining","volume-title":"Proceedings of the 3rd Machine Learning in Systems Biology workshop (MLSB)","author":"Saeys","year":"2009"},{"issue":"Suppl. 2","key":"2023012508080763700_B33","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/gb-2008-9-s2-s2","article-title":"Overview of BioCreative II gene mention recognition","volume":"9","author":"Smith","year":"2008","journal-title":"Genome Biol."},{"issue":"Suppl. 1","key":"2023012508080763700_B34","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1471-2105-6-S1-S3","article-title":"GENETAG: a tagged corpus for gene\/protein named entity recognition","volume":"6","author":"Tanabe","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012508080763700_B35","first-page":"222","article-title":"Syntax annotation for the GENIA corpus","volume-title":"Proceedings of the IJCNLP 2005, Companion volume","author":"Tateisi","year":"2005"},{"key":"2023012508080763700_B36","first-page":"49","article-title":"Sentence and token splitting based on conditional random fields","volume-title":"Proceedings of the 10th Conference of the Pacific Association for Computational Linguistics","author":"Tomanek","year":"2007"},{"key":"2023012508080763700_B37","first-page":"1453","article-title":"Large margin methods for structured and interdependent output variables","volume":"6","author":"Tsochantaridis","year":"2005","journal-title":"J. Mach. Learn. Res."},{"key":"2023012508080763700_B38","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1186\/1471-2105-10-403","article-title":"Investigating heterogeneous protein annotations toward cross-corpora utilization","volume":"10","author":"Wang","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 1","key":"2023012508080763700_B39","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-6-S1-S2","article-title":"BioCreAtIvE task 1A: gene mention finding evaluation","volume":"6","author":"Yeh","year":"2005","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/12\/i382\/48857088\/bioinformatics_26_12_i382.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/12\/i382\/48857088\/bioinformatics_26_12_i382.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:12:30Z","timestamp":1674634350000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/12\/i382\/282442"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,1]]},"references-count":39,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2010,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq180","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,6,15]]},"published":{"date-parts":[[2010,6,1]]}}}