OPEN ACCESS ARTICLE

This Article Free via Open Access: OA OA Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (11) Citing Articles via Google Scholar Google Scholar Articles by Kurata, N. Articles by Yamazaki, Y. Search for Related Content PubMed PubMed Citation Articles by Kurata, N. Articles by Yamazaki, Y. Agricola Articles by Kurata, N. Articles by Yamazaki, Y.

BIOINFORMATICS

Oryzabase. An Integrated Biological and Genome Information Database for Rice^1,[OA]

Genetic Strains Research Center (N.K.) and Center for Genetic Resource Information (Y.Y.), National Institute of Genetics, Mishima, Shizuoka 411–8540, Japan; and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411–8540, Japan (N.K., Y.Y.)

The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Nori Kurata (nkurata{at}lab.nig.ac.jp).

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.063008.

^* Corresponding author; e-mail nkurata{at}lab.nig.ac.jp; fax 81–55–981–6879.

Received March 17, 2005; returned for revision November 2, 2005; accepted November 2, 2005.

This article has been cited by other articles:

				K. L. Childs Genomic and Genetic Database Resources for the Grasses Plant Physiology, January 1, 2009; 149(1): 132 - 136. [Full Text] [PDF]

				V. Shulaev, S. S. Korban, B. Sosinski, A. G. Abbott, H. S. Aldwinckle, K. M. Folta, A. Iezzoni, D. Main, P. Arus, A. M. Dandekar, et al. Multiple Models for Rosaceae Genomics Plant Physiology, July 1, 2008; 147(3): 985 - 1003. [Abstract] [Full Text] [PDF]

				S. Avraham, C.-W. Tung, K. Ilic, P. Jaiswal, E. A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S. Y Rhee, M. M Sachs, et al. The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations Nucleic Acids Res., January 11, 2008; 36(suppl_1): D449 - D454. [Abstract] [Full Text] [PDF]

				S. Mano, T. Miwa, S.-i. Nishikawa, T. Mimura, and M. Nishimura The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research Nucleic Acids Res., January 11, 2008; 36(suppl_1): D929 - D937. [Abstract] [Full Text] [PDF]

				P. Larmande, C. Gay, M. Lorieux, C. Perin, M. Bouniol, G. Droc, C. Sallaud, P. Perez, I. Barnola, C. Biderre-Petit, et al. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1022 - D1027. [Abstract] [Full Text] [PDF]

				A. Masoudi-Nejad, S. Goto, R. Jauregui, M. Ito, S. Kawashima, Y. Moriya, T. R. Endo, and M. Kanehisa EGENES: Transcriptome-Based Plant Database of Genes with Metabolic Pathway Information and Expressed Sequence Tag Indices in KEGG Plant Physiology, June 1, 2007; 144(2): 857 - 866. [Abstract] [Full Text] [PDF]