Aggregating automatically extracted regulatory pathway relations

IEEE Transactions on Information Technology in Biomedicine

Volumn 10, Issue 1, 2006, Pages 100-108

  Marshall, Byron ^a   Su, Hua ^b   McDonald, Daniel ^b   Eggers, Shauna ^b   Chen, Hsinchun ^b  

^a OREGON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

Knowledge representation; Regulatory pathway analysis; Relation parsing

Indexed keywords

ABSTRACTING; BIOMEDICAL ENGINEERING; FINITE AUTOMATA; INDEXING (OF INFORMATION); OBJECT RECOGNITION; SYSTEMS ANALYSIS; TEXTBOOKS;

BIOMEDICAL TEXTS; EXTRACTION SYSTEMS; FEATURE ASSIGNMENT ACCURACY; REGULATORY PATHWAY ANALYSIS; RELATION PARSING;

KNOWLEDGE REPRESENTATION;

PROTEOME;

ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; INFORMATION RETRIEVAL; LINGUISTICS; METABOLISM; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; PUBLICATION; SIGNAL TRANSDUCTION;

ARTIFICIAL INTELLIGENCE; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PROTEOME; PUBLICATIONS; SIGNAL TRANSDUCTION; VOCABULARY, CONTROLLED;

EID: 30744446204     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2005.856857     Document Type: Article

References (18)

1. A. Rzhetsky, I. Iossifov, T. Koike, M. Krauthammer, P. Kra, M. Morris, H. Yu, P. A. Duboue, W. Weng, W. J. Wilbur, V. Hatzivassiloglou, and C. Friedman, "GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data," J. Biomed. Infor., vol. 37, pp. 43-53, 2004.
2. J. C. Park, H. S. Kim, and J. J. Kim, "Bidirectional incremental parsing for automatic pathway identification with combinatory categorical grammar," Paper presented at Pac. Symp. Biocomput., Big Island, HI, 2001, pp. 396-407.
3. M. Palakal, M. Stephens, S. Mukhopadhyay, R. Raje, and S. Rhodes, "Identification of biological relationships from text documents using efficient computational methods," J. Bioinform. Comput. Biol., vol. 1, pp. 307-342, 2003.
4. R. Gaizauskas, G. Demetriou, P. Artymiuk, and P. Willett, "Protein structures and information extraction from biological texts: The PASTA system," Bioinformatics, vol. 19, pp. 135-143, 2003.
5. C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky, "GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles," Bioinformatics, vol. 17, pp. S74-S82, 2001.
6. J. Pustejovsky, J. Castano, J. Zhang, M. Kotecki, and B. Cochran, "Robust relational parsing over biomedical literature: Extracting inhibit relations," Paper presented at Pac. Symp. Biocomput., Lihue, HI, 2002, pp. 362-373.
7. T. C. Rindflesch, L. Tanabe, J. N. Weinstein, and L. Hunter, "EDGAR: Extraction of drugs, genes and relations from the biomedical literature," Paper presented at Pac. Symp. Biocomput., Big Island, HI, 2000, pp. 517-528.
8. G. Leroy, H. Chen, and J. D. Martinez, "A shallow parser based on closed-class words to capture relations in biomedical text," J. Biomed. Inform., vol. 36, pp. 145-158, 2003.
9. D. M. McDonald, H. Chen, H. Su, and B. B. Marshall, "Extracting gene pathway relations using a hybrid grammar: The arizona relation parser," Bioinformatics, vol. 20, no. 18, pp. 3370-3378, 2004.
10. G. R. G. Lanckriet, M. Deng, N. Cristianini, M. I. Jordan, and W. S. Noble, "Kernel-based data fusion and its application to protein function prediction in yeast," Paper presented at Pac. Symp. Biocomput., Big Island, HI, 2004, pp. 300-311.
11. O. Tuason, L. Chen, H. Liu, J. A. Blake, and C. Friedman, "Biological nomenclatures: A source of lexical knowledge and ambiguity," Paper presented at Pac. Symp. Biocomput., Big Island, HI, 2004, pp. 238-249.
12. A. S. Yeh, L. Hirschman, M. Morris, and M. Colosimo, BioCreAtIve Task 1A: Gene Mention Finding Evaluation. Bedford, MA: The MITRE Corp., 2004.
13. L. Hirschman, A. A. Morgan, and A. S. Yeh, "Rutabaga by any other name: Extracting biological names," J. Biomed. Inform., vol. 35, pp. 247-259, 2002.
14. A. Koike and T. Takagi, "Gene/protein/family name recognition in biomedical literature," Paper presented at HLT/NAACL BioLINK Workshop., Boston, Massachusetts, 2004, pp. 9-16.
15. P. V. Ogren, K. B. Cohen, G. K. Acquaah-Mensah, J. Eberlein, and L. Hunter, "The compositional structure of gene ontology terms," Paper presented at Pac. Symp. Biocomput., Big Island, HI, 2004, pp. 214-225.
16. K. Fukuda, T. Tsunoda, A. Tamura, and T. Takagi, "Toward information extraction: Identifying protein names from biological papers," Paper presented at Pac. Symp. Biocomput.,Big Island, HI, 1998, pp. 705-716.
17. D. Hanisch, J. Fluck, H. Mevissen, and R. Zimmer, "Playing biology's name game: Identifying protein names in scientific text," Paper presented at Pac. Symp. Biocomput., Lihue, HI, pp. 403-414.
18. B. B. Marshall, H. Su, D. M. McDonald, and H. Chen, "Linking ontological resources using aggregatable substance identifiers to organize extracted relations," Paper presented at Pac. Symp. Biocomput., Big Island, HI, 2005.