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United States Department of Agriculture

Agricultural Research Service

Research Project: CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES

Location: Corn Insects and Crop Genetics Research

Project Number: 3625-21000-052-00
Project Type: Appropriated

Start Date: Mar 21, 2008
End Date: Mar 20, 2013

Objective:
Objective 1: Implement web-accessible computational and visualization tools, including semantic web technologies, to enable comparison and transfer of agronomically important genetic information among soybean and other legume and related dicot species. Objective 2: Continue to curate and enhance SoyBase and the Soybean Breeder’s Toolbox (SBT), more fully integrating the genetic, phenotypic, physical map, and whole-genome sequence data from soybean and other legumes. Objective 3: Coordinate the quality assembly and annotation of the soybean whole-genome sequence.

Approach:
Soybean ontologies will be prepared to describe selected data types from the Soybean Breeders Toolbox (SBT). Data exchange descriptions (“RDF graphs”) will be developed to allow integration of the data into the Virtual Plant Information Network (VPIN). To let researchers transparently find, retrieve, or apply analytical methods to data contained in the SBT, web services will be developed to make these services accessible through a single portal. Soybase and the SBT will be maintained and updated with new data classes as needed. The Williams 82 physical map and the soybean whole genome sequence, new sequence-based data types in SoyBase, and comparative data from other legume will be integrated and displayed. The project works closely with DOE-JGI to enhance the quality of the soybean whole-genome sequence assembly. This will include analysis of sequence-based genetic markers, comparative analyses with other genomes, and various informatic analyses. BL1; Recertified August 20, 2007.

Last Modified: 9/21/2014
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