Detecting Inconsistencies in Large Biological Networks with Answer Set Programming

DOI10.1007/978-3-540-89982-2_19MaRDI QIDQ5504653zbMATH OpenOpenAlexWikidataFDO

Authors Martin Gebser, Torsten Schaub, Sven Thiele, Björn Usadel, Philippe Veber

Publication date 22 January 2009

Published in Logic Programming (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1007.0134

Mathematics Subject Classification ID

Systems biology, networks (92C42) Logic programming (68N17)

Abstract: We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). 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 ASP 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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Cited in

(7)

• scientific article; zbMATH DE number 1950564 (Why is no real title available?)
• Detecting inconsistencies in large biological networks with answer set programming
• Artificial intelligence in biological modelling
• Measuring instability in normal residuated logic programs: discarding information
• Repairing inconsistent answer set programs using rules of thumb: a gene regulatory networks case study
• Constraint Answer Set Solving
• Constrained community-based gene regulatory network inference

Describes a project that uses

Uses Software

• clasp
• Potassco
• zChaff
• Lparse
• Gringo
• Cmodels

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