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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: MaizeGDB Becomes Sequence-centric

Authors
item Sen, Taner
item Andorf, Carson
item Schaeffer, Mary
item Harper, Elisabeth
item Sparks, Michael
item Duvick, Jon -
item Brendel, Volker -
item Cannon, Ethalinda -
item Campbell, Darwin
item Lawrence, Carolyn

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 11, 2009
Publication Date: December 7, 2009
Citation: Sen, T.Z., Andorf, C.M., Schaeffer, M.L., Harper, E.C., Sparks, M., Duvick, J., Brendel, V., Cannon, E., Campbell, D.A., Lawrence, C.J. 2009. MaizeGDB Becomes Sequence-centric. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bap020. p. 1.

Interpretive Summary: MaizeGDB stores data about the crop plant and research model Zea mays ssp. mays. Here we report recent updates to how genome sequence data are represented at http://www.maizegdb.org. Tools are described that help researchers to make use of the genome sequence within the context of existing maps and genotype descriptions, thus integrating the sequence into the pipeline for improving maize.

Technical Abstract: MaizeGDB is the maize research community’s central repository for genetic and genomic information about the crop plant and research model Zea mays ssp. mays. The MaizeGDB team endeavors to meet research needs as they evolve based on researcher feedback and guidance. Recent work has focused on better integrating existing data with sequence information as it becomes available for the B73, Mo17, and Palomero Toluqueño genomes. Major endeavors along these lines include the implementation of a genome browser to graphically represent genome sequences; implementation of POPcorn, a portal ancillary to MaizeGDB that offers access to independent maize projects and will allow BLAST similarity searches of participating projects’ datasets from a single point; and a joint MaizeGDB/PlantGDB project to involve the maize community in genome annotation. In addition to summarizing recent achievements and future plans, this article also discusses specific examples of community involvement in setting priorities and design aspects of MaizeGDB, which should be of interest to other database and resource providers seeking to better engage their users. MaizeGDB is accessible online at http://www.maizegdb.org.

Last Modified: 10/23/2014
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