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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE Title: Sequence Resources at MaizeGDB with Emphasis on POPcorn: A Project Portal for Corn

Authors
item Lawrence, Carolyn
item Cannon, Ethalinda -
item Andorf, Carson
item Campbell, Darwin
item Harper, Elisabeth
item Schaeffer, Mary
item Sen, Taner

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Proceedings
Publication Acceptance Date: February 15, 2010
Publication Date: March 18, 2010
Citation: Lawrence, C.J., Cannon, E.K., Andorf, C.M., Campbell, D.A., Harper, E.C., Schaeffer, M.L., Sen, T.Z. 2010. Sequence Resources at MaizeGDB with Emphasis on POPcorn: A Project Portal for Corn [abstract]. 52nd Maize Genetics Conference Proceedings. p. 32.

Technical Abstract: MaizeGDB is the maize research community’s centralized, long-term repository for genetic and genomic information about the crop plant and model organism Zea mays ssp. mays. The MaizeGDB team endeavors to meet the needs of the maize research community based on feedback and guidance. Recent work has focused on better integrating sequence information as it becomes available for the B73, Mo17, and Palomero Toluqueno genomes into the MaizeGDB resource. Major endeavors along these lines include the implementation and continued development of the MaizeGDB Genome Browser and the creation of POPcorn, an NSF-funded portal accessible via the MaizeGDB website. POPcorn aims to enable maize researchers to leverage all available genetic and genomic data irrespective of where the data are stored. At present, it is challenging to locate all of the resources, and the different sequence-indexed resources must be searched independently. In addition, when a project's funding period ends, the generated data are often lost because they are not moved to long-term repositories; project sites degrade over time and sometimes disappear entirely. The POPcorn project addresses these challenges by providing: (1) a resource for searching for and browsing maize genomics projects and resources; (2) a single resource that uses Web Services and minimal data warehousing to carry out sequence searches (BLAST) that return BLAST outputs and/or data from all participating projects; and (3) a set of tools that enable collaborators to migrate their data to MaizeGDB, the long-term model organism database for maize genetic and genomic information, at their projects' conclusion. POPcorn is a project ancillary to MaizeGDB and may be accessed online at http://www.maizegdb.org/POPcorn.

Last Modified: 11/22/2014
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