The HumanCyc Pathway-Genome Database and Pathway Tools Software as Tools for Imaging and Analyzing Metabolomics Data

Metabolomics analysis provides a window to the phenotypic responses to stimuli, including disease states and drug interventions. These responses are the end result of complex processes encoded by the organism’s genome. This chapter describes a computational set of tools that can be of great assistance in all kinds of studies related to the metabolic network of an organism in the context of genomic information. These tools comprise (1) Pathway/Genome Databases (PGDBs) a high-level, last-generation database that relates metabolic information to an organism’s genome and (2) Pathway Tools, a software suite designed to access and facilitate analysis on the PGDB information. In particular, we describe HumanCyc, the human PGDB, and explore its usefulness in analyzing and extracting knowledge from the data produced by metabolomics, transcriptomics, and other systemic experiments. In the so-called postgenomic era, the lack of sophistication of many biological databases and resources has become a hurdle for the development of complex analytical tools, especially at the systems biology level, and a common complaint by computational molecular biologists. Resources such as HumanCyc and Pathway Tools can change this situation by providing the developer with a computable encoding of biological knowledge and a sophisticated collection of computational tools to access it.