Detecting Inconsistencies in Large Biological Networks with Answer Set Programming

  • Authors:

  • Martin Gebser;Torsten Schaub;Sven Thiele;Björn Usadel;Philippe Veber

  • Affiliations:

  • Institute for Informatics, University of Potsdam, Potsdam, D-14482;Institute for Informatics, University of Potsdam, Potsdam, D-14482;Institute for Informatics, University of Potsdam, Potsdam, D-14482;Max Planck Institute of Molecular Plant Physiology, Potsdam, D-14476;Institute for Informatics, University of Potsdam, Potsdam, D-14482

  • Venue:
  • ICLP '08 Proceedings of the 24th International Conference on Logic Programming
  • Year:
  • 2008

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Abstract

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 in the data by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.