GrainGenes 2.0. an improved resource for the small-grains community

Abstract

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.

Figure 1.

The core GrainGenes data classes. The conceptual structure of the GrainGenes database showing primary interconnections between classes. The Reference and Image classes connect to many others.

Figure 2.

Colleague schema in AceDB versus MySQL. Like most data classes in GrainGenes, the simple AceDB data model requires several MySQL tables. ID numbers for a data record, rather than object names, are then referenced by other tables (e.g. the colleagueid row in the tables on the right).

Figure 3.

Report of a colleague record in GrainGenes 2.0. Colleague records contain contact information as well as links to data contributed by the researcher. The left menu bar appears on all GrainGenes 2.0 pages providing a common portal to the database query tools and information available via the Web site.