Deductive Calculation Library for KEGG Pathway Simulation

Wataru Fujibuchi (
Susumu Goto (
Minoru Kanehisa (

Institute for Chemical Research, Kyoto University
Gokasho, Uji, Kyoto 611, Japan


KEGG, Kyoto Encyclopedia of Genes and Genomes, project consists of three types of data, pathways, hierarchies, and binary relations, that are used to represent biological knowledge. We present here a C++ library for efficient calculation of possible pathways from binary relations. In practice, the library is used to calculate metabolic pathways from the substrate-product relations of enzymes stored in the LIGAND chemical database for enzyme reactions. The library consists of three modules, the calculation module that is a core part of the library written as an extension of the relational operations, the reaction agent module that converts real chemical reactions to generalized binary relations, and the interface module that accepts deductive operations.