From genomics to chemical genomics: new developments in KEGG

TLDR

The expanding volume of genomic and molecular data underpins the understanding of biological systems and their environmental interactions, and KEGG provides a reference knowledge base linking genomes to biological and chemical spaces through genes, ligands, pathways, and networks. The study aims to computerize functional interpretations within pathway reconstruction by leveraging the hierarchical knowledge of genomic, chemical, and network spaces. KEGG LIGAND has been expanded to include both endogenous and exogenous molecules, with RPAIR offering curated chemical transformation patterns for predicting new reactions and enzyme genes, and drug information now stored separately and linked to KEGG DRUG structure maps. A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases.

Abstract

The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to computerize functional interpretations as part of the pathway reconstruction process based on the hierarchically structured knowledge about the genomic, chemical and network spaces. In accordance with the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both endogenous and exogenous molecules. Specifically, RPAIR contains curated chemical structure transformation patterns extracted from known enzymatic reactions, which would enable analysis of genome-environment interactions, such as the prediction of new reactions and new enzyme genes that would degrade new environmental compounds. Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps.