Abstract
Abstract The field of pathway bioinformatics is concerned with the representation and the manipulation of metabolic information within computers. By organizing genome information into pathways, pathway bioinformatics places genes and their products into a mechanistic framework. This article describes how metabolic pathways are represented in a computer, and it describes the BioCyc (SRI International, Menlo Park, CA) collection of pathway/genome databases for several hundred organisms. Each BioCyc database describes the genome and the metabolic network of a single organism. This article describes computational algorithms for computing with pathway data. Pathway visualization algorithms help scientists comprehend this complex information space and facilitate analysis of large‐scale omics datasets. Pathway analysis algorithms predict the metabolic network of an organism from its genome, identify the genes coding for missing enzymes in metabolic pathways, and enable the comparison of metabolic networks from multiple organisms. They also allow the prediction of the metabolic capabilities of an organism and identify potential drug targets within the metabolic network.
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