KEGG for taxonomy-based analysis of pathways and genomes

TLDR

KEGG (https://www.kegg.jp) is a manually curated database that integrates biological objects across systems, genomics, chemistry, and health information. Each KEGG entry is identified by a kid and accessed via /entry/kid, while pathway, Brite, and genome browsers are launched with /pathway/kid, /brite/kid, and /genome/kid, and taxonomy files and the Brite hierarchy viewer support taxonomy mapping in the KEGG Mapper suite. An improved KO annotation has led to more eukaryotic genomes in KEGG, enhancing taxonomic representation, and taxonomy mapping allows analysis of conserved functional and physical gene linkages across organism groups.

Abstract

Abstract KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.