Biomedical information extraction with predicate-argument structure patterns

CEUR Workshop Proceedings

Volumn 148, Issue , 2005, Pages

  Yakushiji, Akane ^a   Miyao, Yusuke ^a   Tateisi, Yuka ^a,b   Tsujii, Jun'ichi ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC CONSTRUCTION; BIOMEDICAL INFORMATION EXTRACTIONS; CONSTRUCTION ALGORITHMS; CRUCIAL TECHNOLOGY; EXTRACTION RULE; INFORMATION EXTRACTION; LINGUISTIC RULES; LOW COSTS; MACHINE LEARNING TECHNIQUES; PROTEIN-PROTEIN INTERACTIONS;

CHARACTER RECOGNITION; INFORMATION RETRIEVAL; LEARNING SYSTEMS; PROTEINS; SEMANTICS;

EXTRACTION;

EID: 84874333450     PISSN: 16130073     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Christian Blaschke and Alfonso Valencia. The Frame-Based Module of the SUISEKI Information Extraction System. IEEE Intelligent Systems, 17(2):14-20, 2002.
2. Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun Kumar Ramani, and Yuk Wah Wong. Comparative Experiments on Learning Information Extractors for Proteins and their Interactions. Journal Artificial Intelligence in Medicine (Special Issue on Summarization and Information Extraction from Medical Documents), 2004.
3. Nikolai Daraselia, Sergei Egorov, Andrey Yazhuk, Svetlana Novichkova, Anton Yuryev, and Ilya Mazo. Extracting Protein Function Information from MED-LINE Using a Full-Sentence Parser. In Proc. the Second European Workshop on Data Mining and Text Mining for Bioinformatics, pages 15-21, 2004.
4. Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, and Andrey Rzhetsky. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinfor-matics, 17(Suppl. 1):S74-S82, 2001.
5. GENIA Project. GENIA Treebank, 2004. http://www-tsujii.is.s.u-tokyo.ac. jp/GENIA/topics/Corpus/GTB.html.
6. Minlie Huang, Xiaoyan Zhu, Yu Hao, Donald G. Payan, Kunbin Qu, and Ming Li. Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics, 20(18):3604-3612, 2004.
7. Jin-Dong Kim, Tomoko Ohta, Yuka Teteisi, and Jun'ichi Tsujii. GENIA corpus - a semantically annotated corpus for bio-textmining. Bioinformatics, 19(suppl. 1):i180-i182, 2003.
8. Asako Koike, Yoshiyuki Kobayashi, and Toshihisa Takagi. Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource. Genome Research, 13:1231-1243, 2003.
9. G. Leroy and H. Chen. Filling Preposition-Based Templates to Capture Information from Medical Abstracts. In PSB 7, pages 350-361, 2002.
10. Mitchell Marcus, Grace Kim, Mary Ann Marcinkiewicz, Robert MacIntyre, Ann Bies, Mark Ferguson, Karen Katz, and Britta Schasberger. The Penn Treebank: Annotating predicate argument structure. In Proc. AAI '94, 1994.
11. MUC-6. Proc. the Sixth Message Understanding Conference (MUC-6), 1995.
12. Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, and Toshihisa Takagi. Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics, 17(2):155-161, 2001.
13. J. C. Park, H. S. Kim, and J. J. Kim. Bidirectional Incremental Parsing for Automatic Pathway Identification with Combinatory Categorial Grammar. In PSB 6, pages 396-407, 2001.
14. J. Pustejovsky, J. Castano, J. Zhang, M. Kotecki, and B. Cochran. Robust Relational Parsing Over Biomedical Literature: Extracting Inhibit Relations. In PSB 7, pages 362-373, 2002.
15. Ivan A. Sag and Thomas Wasow. Syntactic Theory. CSLI publications, 1999.
16. Kiyoshi Sudo, Satoshi Sekine, and Ralph Grishman. An improved extraction pattern representation model for automatic IE pattern acquisition. In Proc. ACL 2003, pages 224-231, 2003.
17. Joshua M. Temkin and Mark R. Gilder. Extraction of protein interaction information from unstructured text using a context-free grammer. Bioinformatics, 19(16):2046-2053, 2003.
18. Tsujii laboratory. Enju - A practical HPSG parser, 2005. http://www-tsujii.is.s.u-tokyo.ac.jp/enju/.
19. I. Xenarios, E. Fernandez, L. Salwinski, X. J. Duan, M. J. Thompson, E. M. Marcottes, and D. Eisenberg. DIP: The database of interacting proteins: 2001 update. In Nucleic Acids Research, volume 29 (1), pages 239-241, 2001.
20. Akane Yakushiji, Yusuke Miyao, Yuka Tateisi, and Jun'ichi Tsujii. Biomedical information extraction with predicate-argument structure patterns. In Proc. the First International Symposium on Semantic Mining in Biomedicine, 2005. to appear.
21. Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, and Jun'ichi Tsujii. Event Extraction from Biomedical Papers Using a Full Parser. In PSB 6, pages 408-419, 2001.
22. Roman Yangarber, Ralph Grishman, Pasi Tapanainen, and Silja Huttunen. Automatic Acquisition of Domain Knowledge for Information Extraction. In Proc. COLING 2000 - Volume 2, pages 940 - 946, 2000.