This Article 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 ISI 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 ISI Web of Science (2) Citing Articles via Google Scholar Google Scholar Articles by Carollo, V. Articles by Anderson, O. D. Search for Related Content PubMed PubMed Citation Articles by Carollo, V. Articles by Anderson, O. D. Agricola Articles by Carollo, V. Articles by Anderson, O. D.

Bioinformatics

GrainGenes 2.0. An Improved Resource for the Small-Grains Community¹

United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California 94710 (V.C., G.R.L., D.D.H., N.L., D.L.H., O.D.A.); United States Department of Agriculture, Agricultural Research Service, Department of Plant Breeding, Cornell University, Ithaca, New York 14850 (D.E.M.); and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717 (T.K.B.)

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.

² Present address: Children's Hospital Informatics Program, Children's Hospital Boston, 320 Longwood Avenue, Boston, MA 02115.

³ Present address: School of Medicine, Planning and Budgeting, 251 Campus Drive West, Stanford, CA 94305.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.064485.

^* Corresponding author; e-mail vcarollo{at}pw.usda.gov; fax 510–559–5818.

Received April 20, 2005; returned for revision July 10, 2005; accepted August 8, 2005.

This article has been cited by other articles:

				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]