NBRP databases: Databases of biological resources in Japan

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Yamazaki, Yukiko ^a   Akashi, Ryo ^b   Banno, Yutaka ^c   Endo, Takashi ^d   Ezura, Hiroshi ^e   Fukami Kobayashi, Kaoru ^f   Inaba, Kazuo ^e   Isa, Tadashi ^g   Kamei, Katsuhiko ^h   Kasai, Fumie ⁱ   Kobayashi, Masatomo ^f   Kurata, Nori ^a   Kusaba, Makoto ^j   Matuzawa, Tetsuro ^d   Mitani, Shohei ^k   Nakamura, Taro ^l   Nakamura, Yukio ^f   Nakatsuji, Norio ^d   Naruse, Kiyoshi ^m   Niki, Hironori ^a   Nitasaka, Eiji ^c   Obata, Yuichi ^f   Okamoto, Hitoshi ⁿ   Okuma, Moriya ^f   Sato, Kazuhiro ^o   Serikawa, Tadao ^d   Shiroishi, Toshihiko ^a   Sugawara, Hideaki ^a   Urushibara, Hideko ^e   Yamamoto, Masatoshi ^p   Yaoita, Yoshio ^j   Yoshiki, Atsushi ^f   Kohara, Yuji ^a   more..

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b UNIVERSITY OF MIYAZAKI   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d KYOTO UNIVERSITY   (Japan)

^e UNIVERSITY OF TSUKUBA   (Japan)

^f RIKEN   (Japan)

^g NATIONAL INSTITUTE FOR PHYSIOLOGICAL SCIENCES   (Japan)

^h CHIBA UNIVERSITY   (Japan)

ⁱ NATIONAL INSTITUTE FOR ENVIRONMENTAL STUDIES   (Japan)

^j HIROSHIMA UNIVERSITY   (Japan)

^k TOKYO WOMEN'S MEDICAL UNIVERSITY   (Japan)

^l Osaka City University   (Japan)

^m NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

ⁿ RIKEN BRAIN SCIENCE INSTITUTE   (Japan)

^o OKAYAMA UNIVERSITY   (Japan)

^p KYOTO INSTITUTE OF TECHNOLOGY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA BASE; DNA SEQUENCE; INBRED STRAIN; INFORMATION CENTER; INFORMATION RETRIEVAL; INFORMATION TECHNOLOGY; JAPAN; MOLECULAR CLONING; MUTANT; NATIONAL BIORESOURCE PROJECT; ONLINE SYSTEM; ORGANISM; PRIORITY JOURNAL; TRANSGENIC ORGANISM; WILD SPECIES; ALGORITHM; ANIMAL; BIOLOGY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETIC DATABASE; HUMAN; INTERNET; METHODOLOGY; NUCLEIC ACID DATABASE; PLANT GENOME; PROTEIN DATABASE; VIRUS GENOME;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; GENOME, PLANT; GENOME, VIRAL; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; JAPAN; SOFTWARE;

EID: 75549083611     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp996     Document Type: Article

References (28)

1. Benson, A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2009) GenBank. Nucleic Acids Res., 37, D26-D31.
2. Sugawara, H., Ikeo, K., Fukuchi, S., Gojobori, T. and Tateno, Y. (2009) DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res., 37, D16-D18.
3. Blake, J.A., Bult, C.J., Eppig, J.T., Kadin, J.A., Richardson, J.E. and the Mouse Genome Database Group. (2009) The Mouse Genome Database genotypes:phenotypes. Nucleic Acids Res., 37, D712-D719.
4. Dwinell, M.R., Worthey, E.A., Shimoyama, M., Bakir-Gungor, B., DePons, J., Laulederkind, S., Lowry, T., Nigram, R., Petri, V., Smith, J. et al. (2009) The Rat Genome Database 2009: variation, ontologies and pathways. Nucleic Acids Res., 37, D744-D749.
5. Sprague, J., Bayraktaroglu, L., Bradford, Y., Conlin, T., Dunn, N., Fashena, D., Frazer, K., Haendel, M., Howe, D.G., Knight, J. et al. (2008) The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res., 36, D768-D772.
6. Satou, Y., Kawashima, T., Shoguchi, E., Nakayama, A. and Satoh, N. (2005) An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Zoolog Sci., 22, 837-843.
7. Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R. et al. (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res., 37, D555-D559.
8. Rogers, A., Antoshechkin, I., Bieri, T., Blasiar, D., Bastiani, C., Canaran, P., Chan, J., Chen, W.J., Davis, P., Fernandes, J. et al. (2008) WormBase2007. Nucleic Acids Res., 36, D612-D617.
9. Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E.S., Casstevens, T., Hurwitz, B., McCouch, S., Ni, J., Pujar, A. et al. (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res., 36, D947-D953.
10. Mochida, K., Yoshida, T., Sakurai, T., Ogihara, Y. and Shinozaki, K. (2009) TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol., 150, 1135-1146.
11. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Nakao, M., Sasamoto, S., Watanabe, A., Ono, A., Kawashima, K. et al. (2008) Genome structure of the legume, Lotus japonicus. DNA Res., 15, 227-239.
12. Umezawa, T., Sakurai, T., Totoki, Y., Toyoda, A., Seki, M., Ishiwata, A., Akiyama, K., Kurotani, A., Yoshida, T., Mochida, K. et al. (2008) Sequencing and analysis of approximately 40, 000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res., 15, 333-346.
13. Yano, K., Watanabe, M., Yamamoto, N., Tsugane, T., Aoki, K., Sakurai, N. and Shibata, D. (2006) MiBASE: a database of a miniature tomato cultivar Micro-Tom. Plant Biotechnol., 23, 195-198.
14. Hong, E.L., Balakrishnan, R., Dong, Q., Christie, K.R., Park, J., Binkley, G., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G. et al. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res., 36, D577-D581.
15. Hertz-Fowler, C., Peacock, C.S., Wood, V., Aslett, M., Kerhornou, A., Mooney, P., Tivey, A., Berriman, M., Hall, N., Rutherford, K. et al. (2004) GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res., 32, D339-D343.
16. Fey, P., Gaudet, P., Curk, T., Zupan, B., Just, E.M., Basu, S., Merchant, S.N., Bushmanova, Y.A., Shaulsky, G., Kibbe, W.A. et al. (2009) dictyBase-a Dictyostelium bioinformatics resource update. Nucleic Acids Res., 37, D515-D519.
17. Yamazaki, Y., Niki, H. and Kato, J. (2008) Profiling of Escherichia coli Chromosome Database. Methods Mol. Biol., 416, 385-389.
18. Rudd, K.E. (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res., 28, 60-64.
19. Keseler, I.M., Bonavides-Martínez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T. et al. (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res., 37, D464-D470.
20. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedovm, S.I., Nikolskaya, A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41.
21. UniProt Consortium. (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
22. Fukuchi, S., Homma, K., Sakamoto, S., Sugawara, H., Tateno, Y., Gojobori, T. and Nishikawa, K. (2009) The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res., 37, D333-D337.
23. Kanehisa, M., Ataki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
24. Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L. et al. (2009) InterPro: the integrative protein signature database (2009). Nucleic Acids Res., 37, D224-D228.
25. Yamazaki, Y. and Kurata, N. (2006) Oryzabase, An Integrated Biological and Genome Information Database for Rice. Plant Physiol., 140, 12-17.
26. Susan, R.M. and CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative. (2008) Gene nomenclature system for rice. Rice, 1, 72-84.
27. Kato, J. and Hashimoto, M. (2008) Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome. Methods Mol. Biol., 279-293.
28. Mashimo, T., Yanagihara, K., Tokuda, S., Voigt, B., Takizawa, A., Nakajima, R., Kato, M., Hirabayashi, M., Kuramoto, T. and Serikawa, T. (2008) An ENU-iuduced mutant archive for gene targeting in rats. Nat. Genet., 40, 514-515.