NSF funded project: Legume Federation
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The Federated Plant Database Initiative for Legumes (nicknamed "Legume Federation") is an NSF funded project that has an underlying goal of helping to improve agricultural productivity for legumes by integrating genomic, genetic and phenotypic data across species. This is the first of a series of several planned newsletters intended to introduce components and technologies.
The project has four main sub-goals:
  • Encourage knowledge sharing, development, and data exchange among researchers and resource developers working in any legume crop species
  • Define standards for ontology use, data formats, metadata, and web service protocols
  • Establish an open, shared repository for data exchange
  • Support the use of common, open-source genomic and genetic database and website tools
There will be three main phases of the project, which began in Q2 2015: first, to collect and implement a set of technologies and standards for a group of legume database projects with partial funding from the Legume Federation project (including LegumeInfo, Medicago Genome/JCVI, PeanutBase, and SoyBase); second, to share the technologies and standards with other related projects (and adapt and add to the technologies where appropriate); and third, to implement, extend and publicize the technologies and tools for broader use by as wide a user base as possible. 

The project is currently entering the second phase. The newsletter is part of the process of outreach to other key data providers, hosts, and researchers.

You can read more about the project here: ... including tools, technologies and standards. 

Most of the main technologies intentionally come from the GMOD project, and are being extended, in collaboration with other developers and users of these tools. These include JBrowse, GBrowse, Tripal, CMap and InterMine. 

In this first email, we highlight two projects from the first year: 

1) Development of five different
legume InterMine instances. These include: LegumeMine, BeanMine, MedicMine, PeanutMine, and SoyMine.  The Legume Federation is also collaborating with ThaleMine, from the plant model species Arabidopsis.  We will go into detail about the "Mines" in a later email.

2) The Genome Context Viewer (GCV).  This is a new tool developed for intuitive exploration of microsynteny relationships among genomic segments. It relies on the assignment of genome annotations to a standardized set of gene families (development of a robust set of gene families is another goal of the project), and has both server-side and client-side aspects. The server-side component consists of a set of lightweight services that provide genomic segments meeting requirements for candidacy for synteny comparison. The client-side is written exclusively in javascript and is able to aggregate genomic tracks from multiple services, perform alignment and provide interactive display functionality to the user. Code may be found in the github repository and we encourage other groups to consider providing "context search' services for their hosted genomes that may be consumed by other sites, and/or hosting the client on their own websites.

Another major effort, targeted for release at the end of the 2017, is a shared data repository, involving both CyVerse and local data repositories, with metadata formats that will encourage full description of major data sets and systematized description of data provenance and transformations. We will describe these formats and methods in a subsequent email newsletter. 
There are several ways that we would like to invite participation of other groups - including users/researchers, database and web developers, and genetic and genomic data generators. We will be planning a workshop at the Plant and Animal Genome (PAGXXV), probably either on Friday, January 13th (before the conference) or on Tuesday, January 17th.  We will also be contacting groups separately for various development projects and coordination. 

Please contact us at any time if you would like to participate in any way - that is, to:
  • Develop or maintain on-line resources about your research, e.g, QTL data, new maps, new genome sequence, etc.
  • Generate or use data sets for legume species, e.g. protein domain annotation of a set of genes of your interest, etc. 
 Looking forward to new and continuing collaborations with you ...
The Legume Federation group. 
Copyright © 2016 Legume Federation, All rights reserved.

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