Representations of Metabolic Knowledge

Construction of electronic repositories of metabolic information is an increasingly active area of research. Encoding detailed knowledge of a complex biological domain requires finely honed representations. We survey representations used for several metabolic databases, including Eco-Cyc, and reach the following conclusions. Representation of the metabolism must distinguish enzyme classes from individual enzymes, because there is not a one-to-one mapping from enzymes to the reactions they catalyze. Individual enzymes must be represented explicitly as proteins, e.g., by encoding their subunit structure. The species variation of metabolism must be represented. So must the substrate specificity of enzymes, which may be treated in several ways.