The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a primary database resource for understanding the functional meanings and utilities of genomes. It consists of three main databases: PATHWAY, GENES, and LIGAND. PATHWAY contains computerized knowledge on molecular interaction networks, GENES provides information about genes and proteins from genome sequencing projects, and LIGAND offers details on chemical compounds and reactions relevant to cellular processes. Additional databases, EXPRESSION and BRITE, store experimental data and binary relations, respectively. A new database, SSDB, explores protein-coding genes and identifies functional links and ortholog groups. Data objects in KEGG are represented as graphs, and various computational methods are used to detect graph features related to biological functions. KEGG is updated daily and freely available at http://www.genome.ad.jp/kegg/. The introduction highlights the importance of integrating traditional experimental data with new high-throughput technologies, emphasizing the role of graph representation in this integration. The GENES database provides gene annotations, while SSDB offers a graph of best–best relations to identify functional links and ortholog groups. The PATHWAY database contains generalized protein interaction networks, and other databases like LIGAND, EXPRESSION, and BRITE support additional functionalities. Computational tools and resources are also provided by GenomeNet, including DBGET/LinkDB for retrieval and BLAST/FASTA for sequence similarity searches.The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a primary database resource for understanding the functional meanings and utilities of genomes. It consists of three main databases: PATHWAY, GENES, and LIGAND. PATHWAY contains computerized knowledge on molecular interaction networks, GENES provides information about genes and proteins from genome sequencing projects, and LIGAND offers details on chemical compounds and reactions relevant to cellular processes. Additional databases, EXPRESSION and BRITE, store experimental data and binary relations, respectively. A new database, SSDB, explores protein-coding genes and identifies functional links and ortholog groups. Data objects in KEGG are represented as graphs, and various computational methods are used to detect graph features related to biological functions. KEGG is updated daily and freely available at http://www.genome.ad.jp/kegg/. The introduction highlights the importance of integrating traditional experimental data with new high-throughput technologies, emphasizing the role of graph representation in this integration. The GENES database provides gene annotations, while SSDB offers a graph of best–best relations to identify functional links and ortholog groups. The PATHWAY database contains generalized protein interaction networks, and other databases like LIGAND, EXPRESSION, and BRITE support additional functionalities. Computational tools and resources are also provided by GenomeNet, including DBGET/LinkDB for retrieval and BLAST/FASTA for sequence similarity searches.