{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T10:27:29Z","timestamp":1769855249083,"version":"3.49.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,2,9]],"date-time":"2007-02-09T00:00:00Z","timestamp":1170979200000},"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":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-50","type":"journal-article","created":{"date-parts":[[2007,2,9]],"date-time":"2007-02-09T14:08:44Z","timestamp":1171030124000},"source":"Crossref","is-referenced-by-count":259,"title":["BioInfer: a corpus for information extraction in the biomedical domain"],"prefix":"10.1186","volume":"8","author":[{"given":"Sampo","family":"Pyysalo","sequence":"first","affiliation":[]},{"given":"Filip","family":"Ginter","sequence":"additional","affiliation":[]},{"given":"Juho","family":"Heimonen","sequence":"additional","affiliation":[]},{"given":"Jari","family":"Bj\u00f6rne","sequence":"additional","affiliation":[]},{"given":"Jorma","family":"Boberg","sequence":"additional","affiliation":[]},{"given":"Jouni","family":"J\u00e4rvinen","sequence":"additional","affiliation":[]},{"given":"Tapio","family":"Salakoski","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2007,2,9]]},"reference":[{"key":"1422_CR1","unstructured":"PubMed[\n                    http:\/\/www.pubmed.com\/\n                    \n                  ]"},{"issue":"12","key":"1422_CR2","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1093\/bioinformatics\/18.12.1553","volume":"18","author":"L Hirschman","year":"2002","unstructured":"Hirschman L, Park JC, Tsujii J, Wong L, Wu CH: Accomplishments and challenges in literature data mining for biology. Bioinformatics 2002, 18(12):1553\u20131561.","journal-title":"Bioinformatics"},{"issue":"35","key":"1422_CR3","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1089\/106652703322756104","volume":"10","author":"H Shatkay","year":"2003","unstructured":"Shatkay H, Feldman R: Mining the biomedical literature in the genomic era: An overview. Journal of Computational Biology 2003, 10(35):821\u2013855.","journal-title":"Journal of Computational Biology"},{"key":"1422_CR4","first-page":"147","volume-title":"Artificial intelligence and systems biology","author":"KB Cohen","year":"2004","unstructured":"Cohen KB, Hunter L: Natural language processing and systems biology. In Artificial intelligence and systems biology. Edited by: Dubitzky W, Pereira F. Springer-Verlag; 2004:147\u2013175."},{"key":"1422_CR5","unstructured":"Message understanding conference proceedings MUC-7[\n                    http:\/\/www.itl.nist.gov\/iaui\/894.02\/related_projects\/muc\/proceedings\/muc_7_toc.html\n                    \n                  ]"},{"key":"1422_CR6","unstructured":"Text retrieval conference[\n                    http:\/\/trec.nist.gov\/\n                    \n                  ]"},{"key":"1422_CR7","unstructured":"SENSEVAL[\n                    http:\/\/www.senseval.org\/\n                    \n                  ]"},{"key":"1422_CR8","first-page":"73","volume-title":"Proceedings of the Human Language Technology Conference (HLT 2002), San Diego, California","author":"T Ohta","year":"2002","unstructured":"Ohta T, Tateisi Y, Mima H, Tsujii J: GENIA corpus: An annotated research abstract corpus in molecular biology domain. In Proceedings of the Human Language Technology Conference (HLT 2002), San Diego, California Edited by: Marcus M. 2002, 73\u201377."},{"key":"1422_CR9","volume-title":"Parsing English with a link grammar","author":"DD Sleator","year":"1991","unstructured":"Sleator DD, Temperley D: Parsing English with a link grammar. Tech. Rep. CMU-CS-91\u2013196. Department of Computer Science, Carnegie Mellon University, Pittsburgh, PA; 1991."},{"key":"1422_CR10","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3115\/1567594.1567598","volume-title":"Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland","author":"S Pyysalo","year":"2004","unstructured":"Pyysalo S, Ginter F, Pahikkala T, Boberg J, J\u00e4rvinen J, Salakoski T, Koivula J: Analysis of link grammar on biomedical dependency corpus targeted at protein-protein interactions. In Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland Edited by: Collier N, Ruch P, Nazarenko A. 2004, 15\u201321."},{"issue":"6","key":"1422_CR11","first-page":"430","volume":"75","author":"S Pyysalo","year":"2006","unstructured":"Pyysalo S, Ginter F, Pahikkala T, Boberg J, J\u00e4rvinen J, Salakoski T: Evaluation of Two Dependency Parsers on Biomedical Corpus Targeted at Protein-Protein Interactions. Recent Advances in Natural Language Processing for Biomedical Applications, special issue of the International Journal of Medical Informatics 2006, 75(6):430\u2013442.","journal-title":"Recent Advances in Natural Language Processing for Biomedical Applications, special issue of the International Journal of Medical Informatics"},{"key":"1422_CR12","first-page":"89","volume-title":"Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP 05), Borovets, Bulgaria","author":"S Aubin","year":"2005","unstructured":"Aubin S, Nazarenko A, N\u00e9dellec C: Adapting a general parser to a sublanguage. In Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP 05), Borovets, Bulgaria. Edited by: Angelova G, Bontcheva K, Mitkov R, Nicolov N, Nikolov N. Incoma, Bulgaria; 2005:89\u201393."},{"key":"1422_CR13","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-7-S3-S2","volume":"7 Suppl 3","author":"S Pyysalo","year":"2006","unstructured":"Pyysalo S, Salakoski T, Aubin S, Nazarenko A: Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinformatics 2006, 7 Suppl 3: S2.","journal-title":"BMC Bioinformatics"},{"key":"1422_CR14","first-page":"464","volume-title":"Proceedings of the Symposium on Intelligent Data Analysis (IDA 05), Madrid, Spain","author":"E Tsivtsivadze","year":"2005","unstructured":"Tsivtsivadze E, Pahikkala T, Pyysalo S, Boberg J, Myll\u00e4ri A, Salakoski T: Regularized least-squares for parse ranking. In Proceedings of the Symposium on Intelligent Data Analysis (IDA 05), Madrid, Spain Edited by: Famili AF, Kok JN, Pe\u00f1a JM, Siebes A, Feelders AJ. 2005, 464\u2013474."},{"key":"1422_CR15","first-page":"610","volume-title":"Proceedings of The 19th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA\/AIE06), Annecy, France","author":"E Tsivtsivadze","year":"2006","unstructured":"Tsivtsivadze E, Pahikkala T, Boberg J, Salakoski T: Locality-convolution kernel and its application to dependency parse ranking. In Proceedings of The 19th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA\/AIE06), Annecy, France Edited by: Ali M, Dapoigny R. 2006, 610\u2013618."},{"key":"1422_CR16","volume-title":"Proceedings of the ECML\/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06)","author":"T Pahikkala","year":"2006","unstructured":"Pahikkala T, Tsivtsivadze E, Boberg J, Salakoski T: Graph Kernels versus Graph Representations: a Case Study in Parse Ranking. In Proceedings of the ECML\/PKDD'06 workshop on Mining and Learning with Graphs (MLG'06) Edited by: G\u00e4rtner T, Garriga GC, Meinl T. 2006."},{"key":"1422_CR17","unstructured":"The BioInfer webpage[\n                    http:\/\/www.it.utu.fi\/BioInfer\/\n                    \n                  ]"},{"key":"1422_CR18","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. Nature genetics 2000, 25: 25\u201329.","journal-title":"Nature genetics"},{"key":"1422_CR19","unstructured":"BioPAX[\n                    http:\/\/www.biopax.org\/\n                    \n                  ]"},{"key":"1422_CR20","volume-title":"Proceedings of the Workshop on the 1st International Joint Conference on Natural Language Processing (IJCNLP-04)","author":"Y Tateisi","year":"2004","unstructured":"Tateisi Y, Ohta T, Tsujii J: Annotation of Predicate-argument Structure on Molecular Biology Text. In Proceedings of the Workshop on the 1st International Joint Conference on Natural Language Processing (IJCNLP-04) . China; 2004."},{"key":"1422_CR21","first-page":"86","volume-title":"Proceedings of the 36th Annual Meeting of the ACL and the 17th International Conference on Computational Linguistics (COLING-ACL 1998)","author":"CF Baker","year":"1998","unstructured":"Baker CF, Fillmore CJ, Lowe JB: The Berkeley FrameNet project. In Proceedings of the 36th Annual Meeting of the ACL and the 17th International Conference on Computational Linguistics (COLING-ACL 1998). Montreal, Canada; 1998:86\u201390."},{"key":"1422_CR22","first-page":"691","volume-title":"Proceedings of the 17th National Conference on Artificial Intelligence (AAAI-2000)","author":"K Kipper","year":"2000","unstructured":"Kipper K, Dang HT, Palmer M: Class based construction of a verb lexicon. In Proceedings of the 17th National Conference on Artificial Intelligence (AAAI-2000). Austin, USA; 2000:691\u2013696."},{"key":"1422_CR23","first-page":"1989","volume-title":"Proceedings of the 3rd International Conference on Language Resources and Evaluation (LREC-2002)","author":"P Kingsbury","year":"2002","unstructured":"Kingsbury P, Palmer M: From Treebank to PropBank. In Proceedings of the 3rd International Conference on Language Resources and Evaluation (LREC-2002). Las Palmas, Spain; 2002:1989\u20131993."},{"key":"1422_CR24","volume-title":"Proceedings of the Human Language Technology Conference","author":"P Kingsbury","year":"2002","unstructured":"Kingsbury P, Palmer M, Marcus M: Adding Semantic Annotation to the Penn TreeBank. In Proceedings of the Human Language Technology Conference. San Diego, USA; 2002."},{"key":"1422_CR25","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1186\/1471-2105-5-155","volume":"5","author":"T Wattarujeekrit","year":"2004","unstructured":"Wattarujeekrit T, Shah P, Collier N: PASBio: predicate-argument structures for event extraction in molecular biology. BMC Bioinformatics 2004, 5: 155.","journal-title":"BMC Bioinformatics"},{"key":"1422_CR26","first-page":"408","volume-title":"In Proceedings of the sixth Pacific Symposium on Biocomputing (PSB 2001)","author":"A Yakushiji","year":"2001","unstructured":"Yakushiji A, Tateisi Y, Miyao Y, Tsujii J: Event extraction from biomedical papers using a full parser. In Proceedings of the sixth Pacific Symposium on Biocomputing (PSB 2001) 2001, 408\u2013419."},{"key":"1422_CR27","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1109\/TAI.2003.1250226","volume-title":"Proceedings of 15th IEEE International Conference on Tools with Artificial Intelligence","author":"J Ding","year":"2003","unstructured":"Ding J, Berleant D, Xu J, Fulmer AW: Extracting biochemical interactions from MEDLINE using a link grammar parser. In Proceedings of 15th IEEE International Conference on Tools with Artificial Intelligence. Edited by: Werner, B. IEEE Computer Society, Sacramento, California; 2003:467\u2013473."},{"issue":"16","key":"1422_CR28","doi-asserted-by":"publisher","first-page":"2046","DOI":"10.1093\/bioinformatics\/btg279","volume":"19","author":"JM Temkin","year":"2003","unstructured":"Temkin JM, Gilder MR: Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics 2003, 19(16):2046\u20132053.","journal-title":"Bioinformatics"},{"key":"1422_CR29","doi-asserted-by":"publisher","first-page":"43","DOI":"10.3115\/1567594.1567602","volume-title":"Proceedings of the International Workshop on Natural language Processing in Biomedicine and its Applications (JNLPBA)","author":"E Alphonse","year":"2004","unstructured":"Alphonse E, Aubin S, Bessi\u00e9res P, Bisson G, Hamon T, Laguarigue S, Nazarenko A, Manine AP, N\u00e9dellec C, Vetah MOA, Poibeau T, Weissenbacher D: Event-based information extraction for the biomedical domain: The Caderige project. In Proceedings of the International Workshop on Natural language Processing in Biomedicine and its Applications (JNLPBA) Edited by: Collier N, Ruch P, Nazarenko A. 2004, 43\u201349."},{"issue":"5","key":"1422_CR30","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1093\/bioinformatics\/btg452","volume":"20","author":"N Daraselia","year":"2004","unstructured":"Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I: Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 2004, 20(5):604\u2013611.","journal-title":"Bioinformatics"},{"key":"1422_CR31","unstructured":"Link grammar parser and documentation[\n                    http:\/\/www.link.cs.cmu.edu\/link\/\n                    \n                  ]"},{"issue":"67","key":"1422_CR32","first-page":"49","volume":"4","author":"K Franz\u00e9n","year":"2002","unstructured":"Franz\u00e9n K, Eriksson G, Olsson F, Asker L, Lid\u00e9n P, C\u00f6ster J: Protein names and how to find them. International Journal of Medical Informatics. Special issue on Natural Language Processing in Biomedical Applications 2002, 4(67):49\u201361.","journal-title":"International Journal of Medical Informatics. Special issue on Natural Language Processing in Biomedical Applications"},{"key":"1422_CR33","first-page":"639","volume-title":"Proceedings of the 2003 AMIA Annual Symposium, Washington","author":"P Szolovits","year":"2003","unstructured":"Szolovits P: Adding a medical lexicon to an English parser. In Proceedings of the 2003 AMIA Annual Symposium, Washington. Edited by: Musen M. American Medical Informatics Association; 2003:639\u201343."},{"key":"1422_CR34","volume-title":"Workshop on the Evaluation of Parsing Systems, Granada, Spain","author":"D Lin","year":"1998","unstructured":"Lin D: Dependency-based evaluation of MINIPAR. In Workshop on the Evaluation of Parsing Systems, Granada, Spain Edited by: Carroll J. 1998."},{"key":"1422_CR35","unstructured":"Connexor Machinese Syntax[\n                    http:\/\/www.connexor.com\/\n                    \n                  ]"},{"key":"1422_CR36","volume-title":"Tech. Rep. TR 806, Turku Centre for Computer Science (TUCS)","author":"F Ginter","year":"2007","unstructured":"Ginter F, Pyysalo S, Bj\u00f6rne J, Heimonen J, Salakoski T: BioInfer Relationship Annotation Manual. Tech. Rep. TR 806, Turku Centre for Computer Science (TUCS) 2007."},{"key":"1422_CR37","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1177\/001316446002000104","volume":"20","author":"J Cohen","year":"1960","unstructured":"Cohen J: A Coefficient of agreement for nominal scales. Educational and Psychological Measurement 1960, 20: 37\u201346.","journal-title":"Educational and Psychological Measurement"},{"key":"1422_CR38","volume-title":"Nonparametric statistics for the behavioral sciences","author":"S Siegel","year":"1988","unstructured":"Siegel S, Castellan NJ: Nonparametric statistics for the behavioral sciences. 2nd edition. New York: McGraw-Hill; 1988.","edition":"2"},{"issue":"3","key":"1422_CR39","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. Journal of the American Informatics Association 2005, 12(3):296\u2013298.","journal-title":"Journal of the American Informatics Association"},{"key":"1422_CR40","doi-asserted-by":"publisher","first-page":"70","DOI":"10.3115\/1567594.1567610","volume-title":"Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland","author":"J Kim","year":"2004","unstructured":"Kim J, Ohta T, Tsuruoka Y, Tateisi Y, Collier N: Introduction to the bio-entity recognition task at JNLPBA. In Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland Edited by: Collier N, Ruch P, Nazarenko A. 2004, 70\u201375."},{"key":"1422_CR41","unstructured":"Corpora for biomedical natural language processing[\n                    http:\/\/compbio.uchsc.edu\/ccp\/corpora\/\n                    \n                  ]"},{"key":"1422_CR42","doi-asserted-by":"publisher","first-page":"38","DOI":"10.3115\/1641484.1641490","volume-title":"Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, Detroit","author":"KB Cohen","year":"2005","unstructured":"Cohen KB, Fox L, Ogren PV, Hunter L: Corpus design for biomedical natural language processing. In Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, Detroit. Edited by: Cohen KB, Hirschman L, Shatkay H, Blaschke C. ACL; 2005:38\u201345."},{"key":"1422_CR43","unstructured":"Benchmarks and Corpora for BioNLP[\n                    http:\/\/www.informatik.hu-berlin.de\/~hakenber\/links\/benchmarks.html\n                    \n                  ]"},{"key":"1422_CR44","volume-title":"Proceedings of the 4th International Workshop on Linguistically Interpreted Corpora, held at the 10th Conference of the European Chapter of the Association for Computational Linguistics (EACL'03), Budapest","author":"TH King","year":"2003","unstructured":"King TH, Crouch R, Riezler S, Dalrymple M, Kaplan RM: The PARC 700 Dependency Bank. In Proceedings of the 4th International Workshop on Linguistically Interpreted Corpora, held at the 10th Conference of the European Chapter of the Association for Computational Linguistics (EACL'03), Budapest Edited by: Abeille A, Hansen-Schirra S, Uszkoreit H. 2003."},{"key":"1422_CR45","doi-asserted-by":"publisher","first-page":"D449","DOI":"10.1093\/nar\/gkh086","volume":"32","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Research 2004, 32: D449\u2013451.","journal-title":"Nucleic Acids Research"},{"key":"1422_CR46","unstructured":"Database of Interacting Proteins[\n                    http:\/\/dip.doe-mbi.ucla.edu\/\n                    \n                  ]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-50.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-50\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-50.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T04:11:41Z","timestamp":1548216701000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-50"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,2,9]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1422"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-50","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,2,9]]},"article-number":"50"}}