Introduction to KEGG

• Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [pubmed] [pdf]
• Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [pubmed] [pdf] [Thomson]
• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]

Documents

• KEGG Web Links
• KEGG API
• KEGG Markup Language
• KEGG Release Notes
• KEGG Update Notes

References on KEGG

1. Kanehisa, M.; Toward pathway engineering: a new database of genetic and molecular pathways. Science & Technology Japan, No. 59, pp. 34-38 (1996). [pdf]
2. Kanehisa, M. and Goto, S.; A systematic analysis of gene functions by the metabolic pathway database. In "Theoretical and Computational Methods in Genome Research" (Suhai, S., ed.), pp. 41-55, Plenum Press (1997). [ISBN:0-306-45503-X]
3. Goto, S., Bono, H., Ogata, H., Fujibuchi, W., Nishioka, T., Sato, K., and Kanehisa, M.; Organizing and computing metabolic pathway data in terms of binary relations. Pacific Symp. Biocomputing 1997, 175-186 (1996). [pubmed] [pdf]
4. Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997). [pubmed]
5. Kanehisa, M.; Databases of biological information. In "Trends Guide to Bioinformatics" (Brenner, S. and Lewitter, F., eds.), pp. 24-26, Elsevier Science (1998).
6. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34 (1999). [pubmed] [pdf]
7. Kanehisa, M.; KEGG: From genes to biochemical pathways. In "Bioinfomatics: Databases and Systems" (Letovsky, S., ed.), pp. 63-76, Kluwer Academic Publishers (1999). [ISBN:0-7923-8573-X]
8. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]
9. Kanehisa, M.; "Post-genome Informatics", Oxford University Press (2000). [ISBN:0-19-850327-X] [Preface] [Contents]
10. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.; The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002). [pubmed] [pdf]
11. Kanehisa, M. and Goto, S.; KEGG for computational genomics. In "Current Topics in Computational Molecular Biology" (Jiang, T., Xu, Y., and Zhang, M.Q., eds.), pp. 301-315, MIT-Press, Cambridge, MA (2002). [ISBN:0-262-10092-4]
12. Kanehisa, M.; The KEGG database. Novartis Found. Symp. 247, 91-101 (2002). [pubmed]
13. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M.; The KEGG resources for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004). [pubmed] [pdf]
14. Aoki, K.F. and Kanehisa, M.; Using the KEGG Database Resource. In "Current Protocols in Bioinformatics", Unit 1.12, Wiley (2005).
15. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [pubmed] [pdf] [Thomson]
16. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.; KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008). [pubmed] [pdf]
17. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [pubmed] [pdf]

References on Analyses and Algorithms

See the publication list of the Kanehisa Laboratory.

References on DBGET/LinkDB

1. Akiyama, Y., Goto, S., Uchiyama, I., and Kanehisa, M.; WebDBGET: an integrated database retrieval system which provides hyper-links among related entries. MIMBD'95: Second Meeting on the Interconnection of Molecular Biology Databases (1995). [pdf]
2. Goto, S., Akiyama, Y., and Kanehisa, M.; LinkDB: a database of cross links between molecular biology databases. MIMBD'95: Second Meeting on the Interconnection of Molecular Biology Databases (1995). [pdf]
3. Kanehisa, M.; Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci. 22, 442-444 (1997). [pubmed]
4. Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.; DBGET/LinkDB: an integrated database retrieval system. Pacific Symp. Biocomputing 1998, 683-694 (1997). [pubmed] [pdf]
5. Fujibuchi, W., Sato, K., Ogata, H., Goto, S., and Kanehisa, M.; KEGG and DBGET/LinkDB: Integration of biological relationships in divergenet molecular biology data. In "Knowledge Sharing Across Biological and Medical Knowledge Based Systems", Technical Report WS-98-04, pp. 35-40, AAAI Press (1998).

References on LIGAND

1. Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database for enzyme reactions. Bioinformatics 14, 591-599 (1998). [pubmed]
2. Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND database for enzymes, compounds, and reactions. Nucleic Acids Res. 27, 377-379 (1999). [pubmed]
3. Goto, S., Nishioka, T., and Kanehisa, M.; LIGAND: chemical database of enzyme reactions. Nucleic Acids Res. 28, 380-382 (2000). [pubmed]
4. Goto, S., Okuno, Y., Hattori, M., Nishioka, T. and Kanehisa, M.; LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404 (2002). [pubmed]

Reference on GLYCAN

1. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., and Kanehisa, M.; KEGG as a glycome informatics resource. Glycobiology 16, 63R-70R (2006). [pubmed]

Project Team

• Project Leader: Minoru Kanehisa
• Biological processes and diseases: Mao Tanabe, Atsuko Yano, Aya Ito, Akiko Hashiguchi, Mika Hirakawa
• Drug information: Mari Watanabe, Makiko Ogata, Fumi Kiuchi
• Small molecule metabolism: Tomoko Komeno, Rumiko Yamamoto, Yuriko Matsuura, Atsuko Yoda, Waka Masuyama, Masahiro Hattori, Masaaki Kotera
• Glycan/lipid metabolism: Masami Hamajima
• Plant metabolism: Hiromi Kinoshita, Toshiaki Tokimatsu
• KO grouping: Miho Furumichi
• Genome/pathway annotation: Tomomi Kamiya, Mayo Ishii, Shiho Ikeuchi, Kanae Morishima, Etsuko Sano
• System Development: Yoko Sato (FJQS), Masayuki Kawasima (FJQS), Junya Ohori (FJQS), Satoshi Miyazaki (FNS), Koichi Ohkubo (SGI), Hideya Uehara (SGI), Kentaro Ozawa (SGI), Susumu Goto, Toshiaki Katayama, Shuichi Kawashima
• Public relations: Miwako Karikomi, Yuko Kato
• Administrative assistants: Kaede Yukawa, Junko Nishida

Acknowledgments

• Bioinformatics Research and Development (2006-2010) of the Japan Science and Technology Agency

• Bioinformatics Center, the Institute for Chemical Research, Kyoto University

• Grand-in-aid for scientific research on the priority area "Genome Informatics" (1995) from the Ministry of Education
• Grand-in-aid for scientific research on the priority area "Genome Science" (1996-2000) from the Ministry of Education
• Research for the Future Program (2000-2004) from the Japan Society for the Promotion of Science
• Bioinformatics Research and Development (2001-2005) of the Japan Science and Technology Agency
• 21st Century COE Program "Genome Science" (2003-2007) from the Ministry of Education
• Grant-in-aid for scientific research on the priority area "Comprehensive Genomics" (2005-2009) from the Ministry of Education