title: From genomics to chemical genomics: new developments in KEGG.
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.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan. kanehisa@kuicr.kyoto-u.ac.jp
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hattori
authors.forename: Kiyoko F
authors.initials: KF
authors.lastname: Aoki-Kinoshita
authors.forename: Masumi
authors.initials: M
authors.lastname: Itoh
authors.forename: Shuichi
authors.initials: S
authors.lastname: Kawashima
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Katayama
authors.forename: Michihiro
authors.initials: M
authors.lastname: Araki
authors.forename: Mika
authors.initials: M
authors.lastname: Hirakawa
mesh_terms: D001711:Biotransformation; D055598:Chemical Phenomena; D002621:Chemistry; D016208:Databases, Factual; D030541:Databases, Genetic; D004777:Environment; D004798:Enzymes / Q000737:chemistry / Q000235:genetics; D023281:Genomics; D006801:Humans; D020407:Internet; D008024:Ligands; D004364:Pharmaceutical Preparations / Q000737:chemistry / Q000145:classification; D015398:Signal Transduction; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D004798:Enzymes; D008024:Ligands; D004364:Pharmaceutical Preparations