Identifying Interaction Sentences from Biological Literature Using Automatically Extracted Patterns

BioNLP 2009 - Biomedical Natural Language Processing Workshop, BioNLP 2009 - held in conjunction with 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, NAACL-HLT 2009 - Proceedings

Volumn , Issue , 2009, Pages 133-141

  Liu, Haibin ^a   Blouin, Christian ^a   Kešelj, Vlado ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL LINGUISTICS; GENETIC ALGORITHMS; MOLECULAR BIOLOGY;

BIOLOGICAL LITERATURES; CLASSIFICATION PERFORMANCE; CLASSIFICATION TASKS; INNOVATIVE COMPONENT; PAIRWISE ALIGNMENT; PART OF SPEECH; PART-OF-SPEECH TAGGER; PART-OF-SPEECH TAGS; SCIENTIFIC LITERATURE; SCORING SCHEMES;

ALIGNMENT;

EID: 84870321157     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (18)

1. Christian Blaschke, Miguel A. Andrade, Christos Ouzounis, and Alfonso Valencia. 1999. Automatic extraction of biological information from scientific text: Protein-protein interactions. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, pages 60-67. AAAI Press.
2. Razvan Bunescu, Ruifang Ge, Rohit J Kate, EdwardMMarcotte, Raymond J Mooney, Arun K Ramani, and Yuk W Wong. 2005. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine, 33(2):139-155.
3. Keh-Jiann Chen, Wen Tsuei, and Lee-Feng Chien. 1998. Pat-trees with the deletion function as the learning device for linguistic patterns. In Proceedings of the 17th international conference on Computational linguistics, pages 244-250, Morristown, NJ, USA. Association for Computational Linguistics.
4. Lee-Feng Chien. 1997. Pat-tree-based keyword extraction for chinese information retrieval. SIGIR Forum, 31(SI):50-58.
5. Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Genome Research, 11(8):1425-1433.
6. Anna Divoli and Teresa K. Attwood. 2005. Bioie: Extracting informative sentences from the biomedical literature. Bioinformatics, 21(9):2138-2139.
7. John E. Freund and Benjamin M. Perles. 2006. Modern Elementary Statistics. Prentice Hall.
8. Jorg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, and Dietrich Rebholz-Schuhmann. 2005. Lll'05 challenge: Genic interaction extraction with alignments and finite state automata. In Proceedings of Learning Language in LogicWorkshop (LLL'05) at ICML, page 38C45, Bonn, Germany.
9. Minlie Huang, Xiaoyan Zhu, Yu Hao, Donald G. Payan, Kunbin Qu, and Ming Li. 2004. Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics, 20:3604-3612.
10. Hyunchul Jang, Jaesoo Lim, Joon-Ho Lim, Soo-Jun Park, Kyu-Chul Lee, and Seon-Hee Park. 2006. Finding the evidence for protein-protein interactions from pubmed abstracts. Bioinformatics, 22(14):e220-e226.
11. Sittichai Jiampojamarn, Nick Cercone, and Vlado Kešelj. 2005. Biological Named Entity Recognition using Ngrams and Classification Methods. In Proceedings of the Conference Pacific Association for Computational Linguistics, PACLING'05, Tokyo, Japan.
12. Jiao Li, Xian Zhang, Yu Hao, Minlie Huang, and Xiaoyan Zhu. 2005. Learning domain-specific knowledge from context-thuir at trec2005 genomics track. In Proceedings of 14th Text Retrireval Conference (TREC2005), Gaithersburg, USA.
13. Alexa T. Mccray and Olivier Bodenreider. 2002. A conceptual framework for the biomedical domain. In Semantics of Relationships, Kluwer, pages 181-198. Kluwer Academic Publishers. Andrei Mikheev. 2002. Periods, capitalized words, etc. Comput. Linguist., 28(3):289-318.
14. Donald R. Morrison. 1968. Patricia - Practical Algorithm To Retrieve Information Coded in Alphanumeric. Journal of the ACM, 15(4):514-534.
15. Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, and Toshihisa Takagi. 2001. Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics, 17(2):155-161.
16. Conrad Plake, Jorg Hakenberg, and Ulf Leser. 2005. Learning patterns for information extraction from free text. In Proceedings of AKKD 2005, Karlsruhe, Germany.
17. Lance Ramshaw and Mitch Marcus. 1995. Text chunking using transformation-based learning. In Proceedings of the Third Workshop on Very Large Corpora, pages 82-94, Somerset, New Jersey.
18. Soumya Raychaudhuri. 2006. Computational Text Analysis: For Functional Genomics and Bioinformatics. Oxford University Press. Andre Skusa, Alexander Ruegg, and Jacob Kohler. 2005. Extraction of biological interaction networks from scientific literature. Brief Bioinform, 6(3):263-276.