Metabolic network expansion with answer set programming

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. © 2009 Springer Berlin Heidelberg.