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.
Author details: | Martin GebserORCiD, Torsten SchaubORCiDGND, Sven Thiele, Philippe Veber |
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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 |