Location: Corn Insects and Crop Genetics Research
Project Number: 5030-21000-069-002-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2017
End Date: Jun 30, 2022
Develop and serve visualization and data access interfaces and analysis tools for the Legume Information System (legumeinfo.org) database and web portal, with emphasis on agronomically relevant genomic data and translational application of model plant data. The Legume Information System 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 needs to accommodate multiple complete genome sequences and large quantities of other genomic data. Objectives include development of visualization systems for cross-species analysis of genetic and genomic features and traits, and tools for visualizing and analyzing variation in breeding data for species of interest. Such visualizations include genetic map viewers for genetic markers and mapped traits, "haplotype" viewers for genetic variants within a species (may include a "pangenome" viewer for visualizing the relationships of genes across a set of sequenced genomes), synteny viewers for comparing genomic structure between species, geographic information viewers for exploring the locations of wild-collected plant varieties, gene family viewers for collections of evolutionarily related genes, and search interfaces for accessing data of various types. Related work in the project involves 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.
The cooperator will work with the ARS-PI to continue incorporation of relevant data from other funded projects; will continue to develop 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 legume species with sequenced genomes; will work with groups such as the International Peanut Genome Consortium 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 emerging diseases of legume crops; and will implement and deliver bioinformatics information and software in accordance with the specifications of the NACA.