Metabolic Network Expansion with Answer Set Programming

Authors:
Torsten Schaub;Sven Thiele
Affiliations:
Institut für Informatik, Universität Potsdam, Potsdam, Germany D-14482;Institut für Informatik, Universität Potsdam, Potsdam, Germany D-14482
Venue:
ICLP '09 Proceedings of the 25th International Conference on Logic Programming
Year:
2009

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Abstract

We propose a qualitative approach to elaborating the biosynthetic capacities of metabolic networks. In fact, large-scale metabolic networks as well as measured datasets suffer from substantial incompleteness. Moreover, traditional formal approaches to biosynthesis require kinetic information, which is rarely available. Our approach builds upon a formal method for analyzing large-scale metabolic networks. Mapping its principles into Answer Set Programming (ASP) allows us to address various biologically relevant problems. In particular, our approach benefits from the intrinsic incompleteness-tolerating capacities of ASP. Our approach is endorsed by recent complexity results, showing that the reconstruction of metabolic networks and related problems are NP-hard.