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Nucleic Acids Res. 2016 Jan 4;44(D1):D1181-8. doi: 10.1093/nar/gkv1159. Epub 2015 Nov 5.

Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family.

Author information

1
National Center for Genome Resources, Santa Fe, NM 87505, USA.
2
Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA.
3
Dept. of Computer Science, Iowa State University, Ames, IA 50011, USA.
4
National Center for Genome Resources, Santa Fe, NM 87505, USA Dept. of Computer Science, Montana State University, Bozeman, MT 59715, USA.
5
USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA.
6
ORISE Fellow, USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA.
7
National Center for Genome Resources, Santa Fe, NM 87505, USA adf@ncgr.org.
8
Dept. of Agronomy, Iowa State University, Ames, IA 50011, USA USDA-ARS Corn Insects and Crop Genetics Research Unit, Crop Genome Informatics Lab, Iowa State University, Ames, IA 50011, USA steven.cannon@ars.usda.gov.

Abstract

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 data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, 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 are 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.

PMID:
26546515
PMCID:
PMC4702835
DOI:
10.1093/nar/gkv1159
[Indexed for MEDLINE]
Free PMC Article

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