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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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Author:Martin GebserORCiD, Torsten SchaubORCiDGND, Sven Thiele, Philippe Veber
ISSN:1471-0684 (print)
Parent Title (English):Theory and practice of logic programming
Publisher:Cambridge Univ. Press
Place of publication:New York
Document Type:Article
Year of first Publication:2011
Year of Completion:2011
Release Date:2017/03/26
Tag:answer set programming; bioinformatics; consistency; diagnosis
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 publication:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Informatik
Notes extern:Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 561