The KEGG resource provides a comprehensive knowledge base for linking genomes to biological systems, including building blocks in the genomic space (KEGG GENES) and chemical space (KEGG LIGAND), as well as wiring diagrams of interaction and reaction networks (KEGG PATHWAY). A new component, KEGG BRITE, has been added to support functional interpretation and pathway reconstruction based on hierarchical knowledge of genomic, chemical, and network spaces. The scope of KEGG LIGAND has been expanded to include both endogenous and exogenous molecules, with RPAIR containing curated chemical structure transformation patterns for analyzing genome-environment interactions. Drug information is now stored separately and linked to KEGG DRUG structure maps. KEGG is a database resource for understanding higher-order functions and utilities of biological systems from genomic and molecular information. It represents biological systems as nested and line graphs, which are used for pathway reconstruction and functional inference. The BRITE database provides hierarchies and binary relations for automating functional interpretations and assisting in the discovery of empirical rules involving genome-environment interactions. The PATHWAY database contains manually drawn pathway maps for metabolism, genetic information processing, and human diseases. The GENES database includes gene catalogs for complete and partial genomes, with manual KO assignments. The KO system classifies orthologous genes and paralogous gene groups, enabling the understanding of the entire genomic space. The LIGAND database has expanded to include components such as REACTION, GLYCAN, RPAIR, and DRUG, reflecting efforts to understand the chemical space. The RC system in the chemical space is a counterpart of the KO system in the genomic space, categorizing chemical structure transformation patterns. The RPAIR database is under development and serves as the basis for the RC system. Glycosyltransferase reactions are analyzed using the KEGG GLYCAN tool, which converts genomic or transcriptomic data to glycan structure variations based on curated glycosyltransferase reactions. KEGG is accessible via the web and FTP, with an API service for programmatic access. KegArray and KegDraw are standalone Java applications for microarray data analysis and glycan structure drawing. The KEGG project is supported by various Japanese research institutions and funding bodies.The KEGG resource provides a comprehensive knowledge base for linking genomes to biological systems, including building blocks in the genomic space (KEGG GENES) and chemical space (KEGG LIGAND), as well as wiring diagrams of interaction and reaction networks (KEGG PATHWAY). A new component, KEGG BRITE, has been added to support functional interpretation and pathway reconstruction based on hierarchical knowledge of genomic, chemical, and network spaces. The scope of KEGG LIGAND has been expanded to include both endogenous and exogenous molecules, with RPAIR containing curated chemical structure transformation patterns for analyzing genome-environment interactions. Drug information is now stored separately and linked to KEGG DRUG structure maps. KEGG is a database resource for understanding higher-order functions and utilities of biological systems from genomic and molecular information. It represents biological systems as nested and line graphs, which are used for pathway reconstruction and functional inference. The BRITE database provides hierarchies and binary relations for automating functional interpretations and assisting in the discovery of empirical rules involving genome-environment interactions. The PATHWAY database contains manually drawn pathway maps for metabolism, genetic information processing, and human diseases. The GENES database includes gene catalogs for complete and partial genomes, with manual KO assignments. The KO system classifies orthologous genes and paralogous gene groups, enabling the understanding of the entire genomic space. The LIGAND database has expanded to include components such as REACTION, GLYCAN, RPAIR, and DRUG, reflecting efforts to understand the chemical space. The RC system in the chemical space is a counterpart of the KO system in the genomic space, categorizing chemical structure transformation patterns. The RPAIR database is under development and serves as the basis for the RC system. Glycosyltransferase reactions are analyzed using the KEGG GLYCAN tool, which converts genomic or transcriptomic data to glycan structure variations based on curated glycosyltransferase reactions. KEGG is accessible via the web and FTP, with an API service for programmatic access. KegArray and KegDraw are standalone Java applications for microarray data analysis and glycan structure drawing. The KEGG project is supported by various Japanese research institutions and funding bodies.