Location: Corn Insects and Crop Genetics ResearchTitle: Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family
|Dash, Sudhansu - National Center For Genome Resources|
|Campbell, Jacqueline - Iowa State University|
|Cannon, Ethalinda - Iowa State University|
|Cleary, Alan - National Center For Genome Resources|
|Huang, Wei - Iowa State University|
|Karingula, Vijay - Iowa State University|
|Rice, Alex - National Center For Genome Resources|
|Singh, Jugpreet - Orise Fellow|
|Umale, Pooja - National Center For Genome Resources|
|Wilkey, Andrew - Iowa State University|
|Farmer, Andrew - National Center For Genome Resources|
Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2015
Publication Date: 11/5/2015
Citation: Dash, S., Campbell, J.D., Cannon, E., Cleary, A.M., Huang, W., Kalberer, S.R., Karingula, V., Rice, A.G., Singh, J., Umale, P.E., Weeks, N.T., Wilkey, A.P., Farmer, A.D., Cannon, S.B. 2015. Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family. 2016. Nucleic Acids Research. 44 (D1):D1181-D1188. doi: 10.1093/nar/gkv1159.
Interpretive Summary: In order to speed the process of crop improvement, researchers are increasingly using low-cost sequencing methods to determine the sequences of genes, genetic markers, or entire genomes (the full chromosome complement of an organism). This information can be used by plant breeders or geneticists to identify genes or markers in plants that are important for traits such as disease resistance, nutritional qualities, or drought tolerance. The Legume Information System (LIS) project, at http://legumeinfo.org, is organizing genetic and genomic information for the group of plants in the legume family, including crops such as soybean, common bean, chickpea, and peanut. This on-line resource gives researchers access to the genome sequences for nine species, and holds information about genetic markers for important crop characteristics. Breeders and other plant researchers will be able to use this information to produce new varieties for farmers and consumers.
Technical Abstract: The Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate datasets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate datasets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species, and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas, and interfaces so that data collected by one legume research community is accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the "Legume Federation" project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs.