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Detecting inconsistencies in large biological networks with answer set programming

Published online by Cambridge University Press:  27 January 2011

MARTIN GEBSER ,
TORSTEN SCHAUB ,
SVEN THIELE  and
PHILIPPE VEBER
MARTIN GEBSER
Affiliation:
Institute for Informatics, University of Potsdam, Potsdam, Germany (e-mail: gebser@cs.uni-potsdam.de, torsten@cs.uni-potsdam.de, sthiele@cs.uni-potsdam.de)
TORSTEN SCHAUB
Affiliation:
Institute for Informatics, University of Potsdam, Potsdam, Germany (e-mail: gebser@cs.uni-potsdam.de, torsten@cs.uni-potsdam.de, sthiele@cs.uni-potsdam.de)
SVEN THIELE
Affiliation:
Institute for Informatics, University of Potsdam, Potsdam, Germany (e-mail: gebser@cs.uni-potsdam.de, torsten@cs.uni-potsdam.de, sthiele@cs.uni-potsdam.de)
PHILIPPE VEBER
Affiliation:
Institut Cochin, Paris, France (e-mail: philippe.veber@googlemail.com)
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Abstract

We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.

Keywords

answer set programmingbioinformaticsconsistencydiagnosis
Type
Regular Papers
Information
Theory and Practice of Logic Programming , Volume 11 , Special Issue 2-3: The 24th International Conference on Logic Programming (ICLP 2008) , March 2011 , pp. 323 - 360
Copyright
Copyright © Cambridge University Press 2011

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