The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a comprehensive knowledge base designed for systematic analysis of gene functions through the study of gene and molecular networks. The primary component, the PATHWAY database, includes graphical diagrams of biochemical pathways, covering metabolic and regulatory pathways. KEGG also maintains the GENES database, which catalogs genes from organisms with complete and partial genomes, and the LIGAND database, which lists chemical compounds and enzymes. Each gene catalog is linked to a graphical genome map for chromosomal locations. KEGG provides computational tools for reconstructing biochemical pathways from genome sequences and predicting gene regulatory networks from gene expression profiles. The databases are updated daily and freely available online. The objectives of KEGG include standardizing gene and protein annotations, providing consistent annotations by linking genes to KEGG pathways, maintaining a catalog of chemical elements and substances, and developing informatics technologies for predicting biological systems and designing experiments. The KEGG databases are organized into pathway and genomic information, with user-friendly navigation and integration with other molecular biology databases. Key features include pathway maps, gene catalogs, genome maps, ortholog group tables, and molecular catalogs. KEGG also offers tools for pathway reconstruction and analysis, including pathway reconstruction from binary relations, which can predict alternative paths and fill missing links in fragmented pathways. The KEGG system is accessible via the internet and can be installed on academic institution servers.The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a comprehensive knowledge base designed for systematic analysis of gene functions through the study of gene and molecular networks. The primary component, the PATHWAY database, includes graphical diagrams of biochemical pathways, covering metabolic and regulatory pathways. KEGG also maintains the GENES database, which catalogs genes from organisms with complete and partial genomes, and the LIGAND database, which lists chemical compounds and enzymes. Each gene catalog is linked to a graphical genome map for chromosomal locations. KEGG provides computational tools for reconstructing biochemical pathways from genome sequences and predicting gene regulatory networks from gene expression profiles. The databases are updated daily and freely available online. The objectives of KEGG include standardizing gene and protein annotations, providing consistent annotations by linking genes to KEGG pathways, maintaining a catalog of chemical elements and substances, and developing informatics technologies for predicting biological systems and designing experiments. The KEGG databases are organized into pathway and genomic information, with user-friendly navigation and integration with other molecular biology databases. Key features include pathway maps, gene catalogs, genome maps, ortholog group tables, and molecular catalogs. KEGG also offers tools for pathway reconstruction and analysis, including pathway reconstruction from binary relations, which can predict alternative paths and fill missing links in fragmented pathways. The KEGG system is accessible via the internet and can be installed on academic institution servers.