Metabolic Reconstruction Databases and Their Application to Metabolomics Research

Abstract

Metabolic reconstruction databases model metabolic knowledge about an organism and facilitate interpretation of metabolomics data. These databases can be extended with findings from metabolomics studies to provide an up-to-date, centralized repository of metabolic knowledge about an organism. This chapter describes the MetaCyc family of Pathway/Genome Databases (PGDBs). Members of this database family were derived from the MetaCyc database, share its curation principles, and rely on a software environment called Pathway Tools for their construction, refinement, querying, and data analysis. The chapter describes how PGDBs are created, and the query, visualization, and metabolomics data analysis tools available for PGDBs.