A knowledge based approach for representing and reasoning about signaling networks

C. Baral, K. Chancellor, N. Tran, Nhan Tran, A. Joy, M. Berens

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

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 NFκB 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.

Original languageEnglish (US)
JournalBioinformatics
Volume20
Issue numberSUPPL. 1
DOIs
StatePublished - 2004
Externally publishedYes

Fingerprint

Systems Biology
Knowledge-based
Language
Reasoning
Knowledge representation
Availability
Planning
Signaling Pathways
Partial Information
Incomplete Information
Knowledge Representation
Methodology

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Medicine(all)
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

A knowledge based approach for representing and reasoning about signaling networks. / Baral, C.; Chancellor, K.; Tran, N.; Tran, Nhan; Joy, A.; Berens, M.

In: Bioinformatics, Vol. 20, No. SUPPL. 1, 2004.

Research output: Contribution to journalArticle

Baral, C. ; Chancellor, K. ; Tran, N. ; Tran, Nhan ; Joy, A. ; Berens, M. / A knowledge based approach for representing and reasoning about signaling networks. In: Bioinformatics. 2004 ; Vol. 20, No. SUPPL. 1.
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