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Bioinformatics 2005 21(Suppl 2):ii213-ii219; doi:10.1093/bioinformatics/bti1134
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Knowledge-based framework for hypothesis formation in biochemical networks

Nam Tran 1,*, Chitta Baral 1, Vinay J. Nagaraj 2,3 and Lokesh Joshi 2,3

1Department of Computer Science and Engineering, Ira A. Fulton School of Engineering, Arizona State University Tempe, AZ 85281, USA
2Harrington Department of Bioengineering, Arizona State University Tempe, AZ 85281, USA
3The Biodesign Institute at Arizona State University Tempe, AZ 85281, USA

*To whom correspondence should be addressed.

Motivation: The current knowledge about biochemical networks is largely incomplete. Thus biologists constantly need to revise or extend existing knowledge. The revision and/or extension are first formulated as theoretical hypotheses, then verified experimentally. Recently, biological data have been produced in great volumes and in diverse formats. It is a major challenge for biologists to process these data to reason about hypotheses. Many computer-aided systems have been developed to assist biologists in undertaking this challenge. The majority of the systems help in finding ‘pattern’ in data and leave the reasoning to biologists. A few systems have tried to automate the reasoning process of hypothesis formation. These systems generate hypotheses from a knowledge base and given observations. A main drawback of these knowledge-based systems is the knowledge representation formalisms they use. These formalisms are mostly monotonic and are now known to be not quite suitable for knowledge representation, especially in dealing with the inherently incomplete knowledge about biochemical networks.

Results: We present a knowledge-based framework for hypothesis formation for biochemical networks. The framework has been implemented by extending BioSigNet-RR—a knowledge based system that supports elaboration-tolerant representation and non-monotonic reasoning. Features of the extended system are illustrated by a case study of the p53 signal network.

Availability: http://www.biosignet.org

Contact: namtran{at}asu.edu


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