Systematic framework for metabolic networks with constrained biological information: analysis and applications

A metabolic network models the relationship among three different groups of constituting elements: reactions, enzymes, and metabolites, from a given set of metabolic pathways integrally related via gene-regulatory mechanisms. Recent pathway/genome databases inevitably require development of a different methodology for including detail in the network-centric approach to answer concrete biological questions [5]. We define six metabolic models with constrained biological information in which a portion of pathway-centric information is retained. In an attempt to identify the underlying rules which guide the integration of the constituents, much of the scientific effort has been focused thenceforth on metabolite-metabolite and enzyme-enzyme metabolic networks [6].