Project Number: 3625-21000-052-03
Project Type: Specific Cooperative Agreement

Start Date: Jun 21, 2007
End Date: Jun 20, 2012

Objective:
Develop, curate, and serve datasets, visualization and analysis tools for legume genomics, with emphasis on agronomically relevant information. The Legume Information System (LIS) acts as both a long-term repository for legume genetic/genomic data (including data generated by NRI projects) and a portal to data maintained primarily at other sites. LIS also provides tools to retrieve, analyze, compare and visualize legume genetic/genomic data. The LIS database and website (http://comparative-legumes.org ) needs to accommodate multiple new complete genome sequences, and large quantities of new data, particularly from high throughput sequencing technologies. Work on LIS in this Agreement will increase its emphasis on portal and search functions, and will provide more convenient access to data at other genome sites, including Soybase. LIS will also be updated to provide comparative tools to allow researchers to explore relationships between species with sequenced genomes or with mature physical maps. Providing easy access to diverse and complex data sets from multiple sites implies the need for common protocols, interfaces, and interoperability. Cooperation with the parent project will involve design and implementation of new designs and common protocols.

Approach:
The cooperator will work with the ADODR to continue incorporation of relevant data from NRI-funded and other projects; will continue to develop and serve the Legume Information System databases and websites; will modify LIS interfaces to offer researchers more powerful and convenient access to legume full genome sequence data; will provide queries and methods to enable traversal from a marker or region in one genome to the corresponding region(s) in another, and to find genomic features of interest among legume resources; will develop an interface to provide access to genome comparisons for the species with sequenced genomes (soybean, Medicago, and Lotus) or with mature physical maps (e.g., Phaseolus and cowpea); will enhance interoperability with other legume databases, e.g., Soybase and The Soybean Breeder’s Toolbox; will continue to develop and use methods to foster interoperability, including semantic web services; will work closely with technical and user oversight groups convened by USDA-ARS and potentially NSF to insure that the project deliverables meet current and anticipated needs such as increased priorities of legume allergens and Asian Soybean Rust; will continue development of high-throughput sequencing analysis methods to assist in the improvement of agronomically relevant traits; will implement and deliver bioinformatics information and software in accordance with the specifications of the SCA.