Published online 17 October 2015 | Minoru Kanehisa1*, Yoko Sato2, Masayuki Kawashima2, Miho Furumichi1 and Mao Tanabe1
The article discusses the KEGG (Kyoto Encyclopedia of Genes and Genomes) database, an integrated resource for biological interpretation of genome sequences and high-throughput data. KEGG includes databases such as KEGG PATHWAY, BRITE, and KEGG GENES, which are used to link genes to high-level functions of the cell and organism. The KEGG Orthology (KO) database stores molecular functions associated with ortholog groups, enabling the extension of experimental evidence across different organisms. Recent improvements include the addition of viruses, plasmids, and an addendum category for functionally characterized proteins not found in complete genomes. New automatic annotation servers, BlastKOALA and GhostKOALA, utilize pangenome data to improve annotation efficiency. KEGG also provides resources for translational bioinformatics, such as antimicrobial resistance and drug interaction networks. The article highlights the importance of experimental evidence in supporting KO assignments and the development of signature modules and signature KOs for characterizing antimicrobial resistance. Additionally, KEGG offers tools for genome and metagenome annotation, facilitating the interpretation of high-level functions from gene sets in genomes.The article discusses the KEGG (Kyoto Encyclopedia of Genes and Genomes) database, an integrated resource for biological interpretation of genome sequences and high-throughput data. KEGG includes databases such as KEGG PATHWAY, BRITE, and KEGG GENES, which are used to link genes to high-level functions of the cell and organism. The KEGG Orthology (KO) database stores molecular functions associated with ortholog groups, enabling the extension of experimental evidence across different organisms. Recent improvements include the addition of viruses, plasmids, and an addendum category for functionally characterized proteins not found in complete genomes. New automatic annotation servers, BlastKOALA and GhostKOALA, utilize pangenome data to improve annotation efficiency. KEGG also provides resources for translational bioinformatics, such as antimicrobial resistance and drug interaction networks. The article highlights the importance of experimental evidence in supporting KO assignments and the development of signature modules and signature KOs for characterizing antimicrobial resistance. Additionally, KEGG offers tools for genome and metagenome annotation, facilitating the interpretation of high-level functions from gene sets in genomes.