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Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.

A knowledge based approach for representing and reasoning about signaling networks

C. Baral 1,*, K. Chancellor 1, N. Tran 1, N.L. Tran 2, A. Joy 2 and M. Berens 2

1 Department of Computer Science and Engineering, Ira A. Fulton School of Engineering, Arizona State University, Tempe, AZ 85281, USA and 2 Translational Genomics Research Institute, 400 N. Fifth Street, Suite 1600, Phoenix, AZ 85004, USA

Received on January 15, 2004; accepted on March 1, 2004

Motivation: In this paper we propose to use recent developments in knowledge representation languages and reasoning methodologies for representing and reasoning about signaling networks. Our approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation. Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations.

Results: Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks. We use a NF{kappa}B related signaling pathway to illustrate the kinds of reasoning and representation that our system can currently do.

Availability: The system is available on the Web at http://www.public.asu.edu/~cbaral/biosignet

Contact: baral{at}asu.edu

* To whom correspondence should be addressed.


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