Event Extraction from Trimmed Dependency Graphs

2009 Biomedical Natural Language Processing Workshop, BioNLP 2009 - Companion Volume: Shared Task on Event Extraction

Volumn , Issue , 2009, Pages 19-27

  Buyko, Ekaterina ^a   Faessler, Erik ^a   Wermter, Joachim ^a   Hahn, Udo ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GRAPHIC METHODS; LEARNING SYSTEMS;

CLASS INFORMATION; DEPENDENCY GRAPHS; EVENT TRIGGER; EVENTS EXTRACTIONS; F1 SCORES; METHODOLOGICAL FRAMEWORKS;

EXTRACTION;

EID: 77950347191     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (16)

1. Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, and Tapio Salakoski. 2008. A graph kernel for protein-protein interaction extraction. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, pages 1-9.
2. Christian Blaschke, Miguel A. Andrade, Christos Ouzounis, and Alfonso Valencia. 1999. Automatic extraction of biological information from scientific text: Protein-protein interactions. In ISMB'99 - Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology, pages 60-67.
3. Ekaterina Buyko, Joachim Wermter, Michael Poprat, and Udo Hahn. 2006. Automatically adapting an NLP core engine to the biology domain. In Proceedings of the Joint BioLINK-Bio-Ontologies Meeting. A Joint Meeting of the ISMB Special Interest Group on Bio-Ontologies and the BioLINK Special Interest Group on Text Data M ining in Association with ISMB, pages 65-68. Fortaleza, Brazil, August 5, 2006.
4. Chih-Chung Chang and Chih-Jen Lin, 2001. LIBSVM: A library for support vector machines. Software available at http://www.csie.ntu.edu. tw/-cjlin/libsvm.
5. Katrin Fundel, Robert Küffner, and Ralf Zimmer. 2007. Relex-relation extraction using dependency parse trees. Bioinformatics, 23(3):365-371.
6. Jörg Hakenberg, Ulf Leser, Conrad Plake, Harald Kirsch, and Dietrich Rebholz-Schuhmann. 2005. LLL'05 challenge: Genic interaction extraction - identification of language patterns based on alignment and finite state automata. In Proceedings of the 4th Learning Language in Logic Workshop (LLL05), pages 38-45.
7. Minlie Huang, Xiaoyan Zhu, Donald G. Payan, Kunbin Qu, and Ming Li. 2004. Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics, 20(18):3604-3612.
8. Sophia Katrenko and Pieter W. Adriaans. 2006. Learning relations from biomedical corpora using dependency trees. In Karl Tuyls, Ronald L. Westra, Yvan Saeys, and Ann Nowé, editors, KDECB 2006 - Knowledge Discovery and Emergent Complexity in Bioinformatics. Revised Selected Papers of the 1st International Workshop., volume 4366 of Lecture Notes in Computer Science, pages 61-80. Ghent, Belgium, May 10, 2006. Berlin: Springer.
9. Jin-Dong Kim, Tomoko Ohta, and Jun'ichi Tsujii. 2008a. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics, 9(10).
10. Seon-Ho Kim, Juntae Yoon, and Jihoon Yang. 2008b. Kernel approaches for genic interaction extraction. Bioinformatics, 24(1):118-126.
11. Rune Sætre, Kenji Sagae, and Jun'ichi Tsujii. 2007. Syntactic features for protein-protein interaction extraction. In Christopher J. O. Baker and Jian Su, editors, LBM 2007, volume 319, pages 6.1-6.14.
12. Kenji Sagae and Jun'ichi Tsujii. 2007. Dependency parsing and domain adaptation with LR models and par ser ensembles. In Proceedings of the CoNLL Shared Task Session of EMNLP-CoNLL 2007, pages 1044-1050.
13. Jasmin Šarić, Lars J. Jensen, Rossitza Ouzounova, Isabel Rojas, and Peer Bork. 2004. Extracting regulatory gene expression networks from pubmed. In ACL '04: Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, page 191, Morristown, NJ, USA. Association for Computational Linguistics.
14. Joachim Wermter, Katrin Tomanek, and Udo Hahn. 2009. High-performance gene name normalization with GeNo. Bioinformatics, 25(6):815-821.
15. Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, and Jun'ichi Tsujii. 2001. Event extraction from biomedical papers using a full parser. In Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Kevin Lauderdale, and Teri E. Klein, editors, PSB 2001 - Proceedings of the 6th Pacific Symposium on Biocomputing, pages 408-419. Maui, Hawaii, USA. January 3-7, 2001. Singapore: World Scientific Publishing.
16. Guodong Zhou and Min Zhang. 2007. Extracting relation information from text documents by exploring various types of knowledge. Information Processing & Management, 43(4):969-982.