A Pathway Finding System for the Cell Signaling Networks Database

Article type: Research Article

Authors: Takai-Igarashi, Takako | Kaminuma, Tsuguchika

Affiliations: Division of Chem-Bio Informatics, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158, Japan

Note: [] Corresponding author: Tel.: +81-3-3700-1141 ext. 296, Fax: +81-3-5717-7180, E-mail: [email protected]

Abstract: We report on a knowledge-based pathway-finding system that builds on the cell-signaling networks database, CSNDB, which we developed previously. This new system, PaF-CSNDB, uses a general inference engine to apply rules for finding and coupling pathways between or around specific biomolecules from the CSNDB database. We show how PaF-CSNDB finds relationships in a large but fragmented collection of cell-signaling knowledge by filtering out and composing together those sections of pathways specified from an extensive and complex set of binary or pair-wise cell-signaling reactions. The system can be accessed over the World Wide Web (http://goc.nihs.go.jp/csndb.html).

Keywords: cellular signal transduction, knowledge-based expert system shell, pathway representation

Journal: In Silico Biology, vol. 1, no. 3, pp. 129-146, 1999