The Federated Plant Database Initiative for the Legumes legumefederation.org The "Legume Federation" ("The Federated Plant Database Initiative for the Legumes") is an NSF project to foster data standards, distributed development, and comparative analysis, via gene families and shared phenotypes, to support research across the legume family – and to support robust agriculture for a world that is significantly legume-fed.

The goals of the Legume Federation include 1) sharing knowledge, development, and data sets across all legume crops; 2) defining standards for data formats, metadata standards, Web service protocols, and ontology use; 3) establishing an open repository for data exchange; and 4) encouraging the use of common, open-source model organism database tools. Clear standards and formats, with templates and tools for data collection and submission, will enable broader participation. Although a major focus of the project is on methods for distributed development, we emphasize that the fundamental mission is to enable improved agricultural productivity for this important group of crop plants by integrating genetic, genomic, and phenotypic data across species to enable identification of common molecular bases for important traits. Steven B. Cannon1

Ethalinda Cannon2

Jacqueline D. Campbell2

Sudhansu Dash3

Wei Huang2

Akshay Yadav2

Gene families and toolsFamilies are based on and link to Phytozome families, but are legume-focused at LegumeInfo.

Kevin H. Feeley1

Jeremy D. DeBarry5

Andrew D. Farmer3

Christopher D. Town4

David Fernandez-Baca2

Nathan T. Weeks1

Andrew Wilkey2

Sam Hokin3

David Grant1

Rex Nelson1

Vivek Krishnakumar4

1 USDA-ARS-CICGRU, Ames, IA2 Iowa State University, Ames, IA3 National Center for Genome Resources, Santa Fe, NM4 J. Craig Venter Institute, Rockville, MD5 University of Arizona, Tucson, AZ

GMOD software components

Tripal is a set of customizable Drupal modules for constructing biological websites.

The Legume Federation project uses existing software components where available, and extends and contributes these as needed. Recent contributions include a new Tripal BLAST interface, and gene family and synteny viewers (below).

... for project news, list of collaborating projects, data sets and templates. In the coming year, a set of itegrative tools will be added, including a multi-site sequence search interface.

Project websites are using both JBrowse and GBrowse for genome browsing.

Chado is a standardized da-tabase schema for storing biological data.

InterMine provides a set of web tools for browsing and searching genomic data across one or many species. Complex queries can be composed intuitively.

To participate, please contact us at http://legumefederation.org/contact

Funding provided by NSF, award #1444806 with in-kind contribution from the USDA ARS, and participation by other projects including iPlant, NCGR, JCVI and others.

Public and private data repository at iPlant.

Genetic maps are dis-played using CMap. A next-generation map browser will be built as part of this project.

Project site ...

Map and trait data at LegumeInfo, PeanutBase, CSFLDB, ...

GBrowse and JBrowse viewers for each species ... featuring synteny tracks to interlink homologous regions

legumefederation.org @LegumeFed

twitter.com/legumefed

and Twitter feed