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Bioinformatics Vol. 17 no. 9 2001
Pages 829-837
© 2001 Oxford University Press

Knowledge representation of signal transduction pathways

Ken-ichiro Fukuda 1,2 and Toshihisa Takagi 1

1 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

Received on December 11, 2000 ; revised on March 7, 2001 ; accepted on April 17, 2001

Motivations: Signal transduction is the common term used to define a diverse topic that encompasses a large body of knowledge about the biochemical mechanisms. Since most of the knowledge of signal transduction resides in scientific articles and is represented by texts in natural language or by diagrams, there is the need of a knowledge representation model for signal transduction pathways that can be as readily processed by a computer as it is easily understood by humans.

Results: A signal transduction pathway representation model is presented. It is based on a compound graph structure and is designed to handle the diversity and hierarchical structure of pathways. A prototype knowledge base was implemented on a deductive database and a number of biological queries are demonstrated on it.

Contact: fukuda-cbrc{at}aist.go.jp; ichiro{at}ims.u-tokyo.ac.jp

2 Present address: Computational Biology Research Center (CBRC), NationalInstitute of Advanced Industrial Science and Technology (AIST) 2-41-6 Aomi, Koutou-ku, Tokyo 135-0064, Japan.


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