KEGG for taxonomy-based analysis of pathways and genomes

This paper describes the KEGG resource, a manually curated database that integrates a range of biological objects categorized into systems, genomic, chemical, and health information. Every database entry is identified by a KEGG identifier (kid), generally a prefix followed by a five-digit number, and can be retrieved by appending path components to the KEGG URL; likewise the pathway map viewer, the Brite hierarchy viewer, and the newly released KEGG genome browser can each be launched through their own URL paths. Together with an improved annotation procedure for KEGG Orthology (KO) assignment, an increasing number of eukaryotic genomes have been included for better representation of organisms in the taxonomic tree.

To enable taxonomy-based analysis, multiple taxonomy files are generated for classifying KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping within the new KEGG Mapper suite. This taxonomy mapping lets researchers analyze questions such as how the functional links of genes within a pathway and the physical links of genes along the chromosome are conserved among different organism groups, extending KEGG's usefulness for comparative genome and pathway analysis across the taxonomic tree.