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Detecting inconsistencies in large biological networks with answer set programming

  • 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.

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Metadaten
Author details:Martin GebserORCiD, Torsten H. SchaubORCiDGND, Sven Thiele, Philippe Veber
DOI:https://doi.org/10.1017/S1471068410000554
ISSN:1471-0684
Title of parent work (English):Theory and practice of logic programming
Publisher:Cambridge Univ. Press
Place of publishing:New York
Publication type:Article
Language:English
Year of first publication:2011
Publication year:2011
Release date:2017/03/26
Tag:answer set programming; bioinformatics; consistency; diagnosis
Volume:11
Issue:5-6
Number of pages:38
First page:323
Last Page:360
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Informatik und Computational Science
Peer review:Referiert
Institution name at the time of the publication:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Informatik
External remark:Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 561
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