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From genomics to chemical genomics: new developments in KEGG
1Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Kyoto 611-0011, Japan 2Human Genome Center, Institute of Medical Science, University of Tokyo Minato-ku, Tokyo 108-8639, Japan 3Institute for Bioinformatics Research and Development, Japan Science and Technology Agency Chiyoda-ku, Tokyo 102-8666, Japan
*To whom correspondence should be addressed. Tel: +81 774 38 3270; Fax: +81 774 38 3269; Email: kanehisa{at}kuicr.kyoto-u.ac.jp
Received September 14, 2005. Revised October 17, 2005. Accepted October 17, 2005.
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.
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K. Degtyarenko, P. de Matos, M. Ennis, J. Hastings, M. Zbinden, A. McNaught, R. Alcantara, M. Darsow, M. Guedj, and M. Ashburner ChEBI: a database and ontology for chemical entities of biological interest Nucleic Acids Res., January 11, 2008; 36(suppl_1): D344 - D350. [Abstract] [Full Text] [PDF]
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T. Nakahara, R. Hashimoto, H. Nakagawa, K. Monde, N. Miura, and S.-I. Nishimura Glycoconjugate Data Bank:Structures an annotated glycan structure database and N-glycan primary structure verification service Nucleic Acids Res., January 11, 2008; 36(suppl_1): D368 - D371. [Abstract] [Full Text] [PDF]
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E. Grafahrend-Belau, S. Weise, D. Koschutzki, U. Scholz, B. H. Junker, and F. Schreiber MetaCrop: a detailed database of crop plant metabolism Nucleic Acids Res., January 11, 2008; 36(suppl_1): D954 - D958. [Abstract] [Full Text] [PDF]
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A. Papanicolaou, S. Gebauer-Jung, M. L. Blaxter, W. Owen McMillan, and C. D. Jiggins ButterflyBase: a platform for lepidopteran genomics Nucleic Acids Res., January 11, 2008; 36(suppl_1): D582 - D587. [Abstract] [Full Text] [PDF]
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L. J. Jensen, P. Julien, M. Kuhn, C. von Mering, J. Muller, T. Doerks, and P. Bork eggNOG: automated construction and annotation of orthologous groups of genes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D250 - D254. [Abstract] [Full Text] [PDF]
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C. Su, J. M. Peregrin-Alvarez, G. Butland, S. Phanse, V. Fong, A. Emili, and J. Parkinson Bacteriome.org an integrated protein interaction database for E. coli Nucleic Acids Res., January 11, 2008; 36(suppl_1): D632 - D636. [Abstract] [Full Text] [PDF]
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S. Gunther, M. Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E. G. Urdiales, A. Gewiess, L. J. Jensen, et al. SuperTarget and Matador: resources for exploring drug-target relationships Nucleic Acids Res., January 11, 2008; 36(suppl_1): D919 - D922. [Abstract] [Full Text] [PDF]
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K. P. Seiler, G. A. George, M. P. Happ, N. E. Bodycombe, H. A. Carrinski, S. Norton, S. Brudz, J. P. Sullivan, J. Muhlich, M. Serrano, et al. ChemBank: a small-molecule screening and cheminformatics resource database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D351 - D359. [Abstract] [Full Text] [PDF]
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