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United States Department of Agriculture

Agricultural Research Service

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Research Project: Legume Information System and Network-a Legume Bioinformatics Resource

Location: Corn Insects and Crop Genetics Research

Project Number: 3625-21000-062-05
Project Type: Specific Cooperative Agreement

Start Date: Jul 01, 2013
End Date: Jun 29, 2015

Objective:
Collect and curate content, develop and serve visualization and data access interfaces and analysis tools for a legume genomic database with emphasis on agronomically relevant genomic data and translational application of model plant data. The Legume Information System (LIS) acts both as a long-term repository for legume genetic and genomic data and as a portal to data maintained at other sites. LIS also provides tools to retrieve, analyze, compare and visualize legume genetic and genomic data. The LIS database and web site (http://comparative-legumes.org) needs to accommodate multiple complete genome sequences and large quantities of other genomic data. Objectives include evaluation and refinement of website navigation and usability; implementation of a new system for storing and reporting information about genetic traits; improvement of tools for sequence search; improvement of the codebase for maintainability; assistance with mirroring of the codebase by the ARS group; coordination of LIS development with other genomic databases (within ARS and externally); improvement of user guides and tutorials; and communication with diverse legume research groups to incorporate and integrate new legume genomic data and adopt common protocols.

Approach:
The cooperator will work with the ARS to continue incorporation of relevant data; will continue to develop and serve the Legume Information System website and data; will modify LIS interfaces to offer researchers more powerful and convenient access to legume genomic 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, common bean, chickpea, Medicago, Lotus) or with ongoing genome projects (e.g. peanut, lupin, or alfalfa); will work with groups to incorporate new legume data; will enhance interoperability with legume and other plant databases and cyberinfrastructure resources; will utilize methods such as developing shared ontologies, and using common data formats and protocols to foster interoperability; will work closely with technical and user oversight groups convened by USDA-ARS and potentially NSF to ensure that the project deliverables meet current and anticipated needs such as increased priorities of legume allergens and Asian Soybean Rust; and will implement and deliver bioinformatics information and software in accordance with the specifications of the SCA.

Last Modified: 10/1/2014
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