Databases of metabolic pathways

Studies of metabolism usually evoke memories of densely written wall charts of metabolic pathways of enormous complexity, such as the IUBMB-Nicholson metabolic pathways map or the Roche metabolic pathways wall chart. Advances in bioinformatics in the past decade have brought about a revolution in the way the information in metabolic pathways is viewed and managed. Today, metabolic pathways are stored in knowledge bases that can be queried, modified, copied, and extended with ease, precision, and speed. Moreover, the flexibility of the digital medium for the presentation of metabolic pathways surpasses the traditional printed form used in classical pathway maps. In digital presentations, the separation of the content from the visual presentation is the norm, implying that metabolic pathway maps can be generated dynamically from the information stored in the knowledge base. The most advanced metabolic pathways databases are freely available over the Internet, and this has important implications for modern studies of metabolic pathways in biochemistry and molecular biology. This study reviews two such databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the BioCyc collection of pathway/genome databases. The background information and the structure of these databases are presented, with the emphasis on BioCyc, which represents a global multicollaborative effort to unify the representation of metabolic pathways.