Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2005
Publication Date: 10/1/2005
Citation: Carollo, V.L., Matthews, D.E., Lazo, G.R., Blake, T.K., Hummel, D., Lui, N., Hane, D.L., Anderson, O.D. 2005. Grain genes 2.0 - an improved resource for the small-grains community. Plant Physiology. 139:643-651. Interpretive Summary: This paper was written by invitation to be included in a plant database focus issue of Plant Physiology. It provides details on the migration of GrainGenes from the former AceDB database software to a new relational database MySQL. Details concerning the migration and data transformation are given. The paper also describes the curation process in GrainGenes. Different data classes require varying amounts of curator input, ranging from nearly automatic to manual. A user perspective is also provided to describe how GrainGenes helps a plant breeder expedite his research. The future of the database and links with other projects are discussed.
Technical Abstract: GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat, barley, rye and their wild relatives) and oat 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, QTLs, 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 website incorporates other more specific databases, informational topics and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat ESTs, EST-SSRs, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate website 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. ---------------------------------------------------------------------------- Server protocol: HTTP/1.1 Remote host: Remote IP address: 184.108.40.206