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 ThieleORCiDGND, Philippe Veber |
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URN: | urn:nbn:de:kobv:517-opus4-412467 |
DOI: | https://doi.org/10.25932/publishup-41246 |
ISSN: | 1866-8372 |
Title of parent work (English): | Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe |
Publication series (Volume number): | Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe (561) |
Publication type: | Postprint |
Language: | English |
Date of first publication: | 2019/01/30 |
Publication year: | 2011 |
Publishing institution: | Universität Potsdam |
Release date: | 2019/01/30 |
Tag: | answer set programming; bioinformatics; consistency; diagnosis |
Issue: | 561 |
Number of pages: | 38 |
Source: | Theory and Practice of Logic Programming 11 (2011) 2–3, pp. 323–360 DOI 10.1017/S1471068410000554 |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät |
DDC classification: | 0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik |
Peer review: | Referiert |
Publishing method: | Open Access |
Grantor: | Cambridge University Press (CUP) |
License (German): | Keine öffentliche Lizenz: Unter Urheberrechtsschutz |
External remark: | Bibliographieeintrag der Originalveröffentlichung/Quelle |