From genomics to chemical genomics: new developments in KEGG

From genomics to chemical genomics: new developments in KEGG

Received September 14, 2005; Revised and Accepted October 17, 2005 | Minoru Kanehisa1,2,* Susumu Goto1, Masahiro Hattori1, Kiyoko F. Aoki-Kinoshita1, Masumi Itoh1, Shuichi Kawashima2, Toshiaki Katayama2, Michihiro Araki2 and Mika Hirakawa1,3
The article discusses the evolution and new developments in the KEGG resource, which is a comprehensive database for understanding higher-order biological systems. The KEGG resource is categorized into four main components: KEGG GENES (building blocks in the genomic space), KEGG LIGAND (building blocks in the chemical space), KEGG PATHWAY (wiring diagrams of interaction networks and reaction networks), and KEGG BRITE (ontologies for pathway reconstruction). The addition of KEGG BRITE provides a logical foundation for inferring higher-order functions. The scope of KEGG LIGAND has been expanded to include both endogenous and exogenous molecules, with RPAIR containing curated chemical structure transformation patterns from enzymatic reactions. The KEGG DRUG database has been introduced to store drug information and link it to new structure maps. The PATHWAY database now includes more regulatory pathways and metabolic pathways, while the GENES database provides gene catalogs for various genomes. The KO system, a pathway-based classification of orthologous genes, is used to link genomic information with network information. The RC system categorizes chemical structure transformation patterns, enabling the automatic assignment of EC numbers and exploration of unknown reactions. The article also highlights the integration of glycomics and the availability of KEGG resources through web, FTP, API, and standalone applications like KegArray and KegDraw.The article discusses the evolution and new developments in the KEGG resource, which is a comprehensive database for understanding higher-order biological systems. The KEGG resource is categorized into four main components: KEGG GENES (building blocks in the genomic space), KEGG LIGAND (building blocks in the chemical space), KEGG PATHWAY (wiring diagrams of interaction networks and reaction networks), and KEGG BRITE (ontologies for pathway reconstruction). The addition of KEGG BRITE provides a logical foundation for inferring higher-order functions. The scope of KEGG LIGAND has been expanded to include both endogenous and exogenous molecules, with RPAIR containing curated chemical structure transformation patterns from enzymatic reactions. The KEGG DRUG database has been introduced to store drug information and link it to new structure maps. The PATHWAY database now includes more regulatory pathways and metabolic pathways, while the GENES database provides gene catalogs for various genomes. The KO system, a pathway-based classification of orthologous genes, is used to link genomic information with network information. The RC system categorizes chemical structure transformation patterns, enabling the automatic assignment of EC numbers and exploration of unknown reactions. The article also highlights the integration of glycomics and the availability of KEGG resources through web, FTP, API, and standalone applications like KegArray and KegDraw.
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[slides and audio] From genomics to chemical genomics%3A new developments in KEGG