K Fukuda1, T Takagi. 1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. fukuda-cbrc@aist.go.jp
Abstract
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.
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.
Authors: Kumaran Kandasamy; S Sujatha Mohan; Rajesh Raju; Shivakumar Keerthikumar; Ghantasala S Sameer Kumar; Abhilash K Venugopal; Deepthi Telikicherla; J Daniel Navarro; Suresh Mathivanan; Christian Pecquet; Sashi Kanth Gollapudi; Sudhir Gopal Tattikota; Shyam Mohan; Hariprasad Padhukasahasram; Yashwanth Subbannayya; Renu Goel; Harrys K C Jacob; Jun Zhong; Raja Sekhar; Vishalakshi Nanjappa; Lavanya Balakrishnan; Roopashree Subbaiah; Y L Ramachandra; B Abdul Rahiman; T S Keshava Prasad; Jian-Xin Lin; Jon C D Houtman; Stephen Desiderio; Jean-Christophe Renauld; Stefan N Constantinescu; Osamu Ohara; Toshio Hirano; Masato Kubo; Sujay Singh; Purvesh Khatri; Sorin Draghici; Gary D Bader; Chris Sander; Warren J Leonard; Akhilesh Pandey Journal: Genome Biol Date: 2010-01-12 Impact factor: 13.583