Functional Genomics Data Society (FGED)

At a Glance
  • Status: Active Consortium
  • Year Launched: 1999
  • Initiating Organization: Stanford University
  • Initiator Type: Academia
  • No disease focus

Abstract

The Functional Genomics Data Society (FGED) works with other organizations to accelerate and support the effective sharing and reproducibility of functional genomics data. FGED facilitates the creation and use of standards and software tools that allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome-wide and other biological research data integration and meta-analysis.

Mission

FGED advocates for open access to genomic datasets and works toward providing concrete solutions to achieve this. The goal is to assure that investment in functional genomics data generates the maximum public benefit. FGED’s work on defining minimum information specifications for reporting data in functional genomics papers have already enabled large datasets to be used and reused to their greater potential in biological and medical research.

FGED works with other organizations to accelerate and support the effective sharing and reproducibility of functional genomics data and facilitates the creation and use of standards and software tools that allow researchers to annotate and share their data easily. FGED promotes scientific discovery that is driven by genome-wide and other biological research data integration and meta-analysis.

Consortium History

November 1999: The MGED Society was founded as a grassroots movement (Nature 2000, 403, 699-700) by many of the major microarray users and developers including Affymetrix, Stanford University, and The European Bioinformatics Institute (EBI).
December 1999: The MGED homepage (www.mged.org) and email discussion groups were established, and first-draft proposals for standards posted (later leading to MIAME and MAGE).
November 2000: A proposal for a microarray data exchange format was submitted to the Object Management Group (OMG).
March 2001: The development of the MAGE standard began in cooperation with many leading companies including Rosetta, Affymetrix, and Agilent.
December 2001: A paper describing MIAME was published in Nature Genetics.
January 2002: The MAGE standard became an Adopted Specification by the OMG.
June 2002: MGED became a nonprofit organization.
October 2002: Several major scientific journals, including the Nature group, The Lancet, Cell, and EMBO, adopted MIAME recommendations as a requirement for publication of microarray experiments.
October 2002: MAGE became the “Available Specification for Gene Expression” at the OMG. A number of implementations have already been developed, including implementations by Affymetrix, the EBI, TIGR, and The University of Pennsylvania.
January 2003: MGED founders announce the creation of Array Express — a public repository for microarray data (Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA, Nucleic Acids Res. 2003 Jan 1;31(1):68-71).
2002-2006: Together with others, MGED helps to push the scientific community toward data standards and more open data sharing by publishing multiple papers on their importance. Today, data sharing is standard policy for many journals and is required of most obtaining National Institutes of Health (NIH) funding.
September 2005: Planning for the Functional Genomics Ontology (FuGO) begins at MGED8 in Bergen, Norway. FuGO expands to become the Ontology for Biomedical Investigations (OBI) in 2006.
November 2006: MGED creates a simplified format for submitting MIAME-compliant microarray data and publishes “A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB” (Rayner et. al., BMC Bioinformatics. 2006 Nov 6;7:489).
March 2008: Workshop of Ultra High Throughput Sequencing stakeholders takes place in Berkeley, California, leading to the Minimum Information about a high-throughput SeQuencing Experiment (MINSEQE).
October 2009: A community service to facilitate data deposition is initiated.
May 2010: Annotare version 1.0 functional genomics annotation tool is released (Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA. Bioinformatics. 2010 Oct 1;26(19):2470-1).
July 2010: The MGED Society changes its name to the Functional Genomics Data Society (FGED) to reflect its current mission, which embraces functional genomics and not just microarrays or gene expression.

Structure & Governance

The bylaws that govern FGED can be found at http://fged.org/about-us/by-laws/

FGED is governed by a Board of Directors, B.F. Francis Ouellette (president), Ronald Taylor (treasurer), and Steve Chervitz Trutane (secretary).

Impact/Accomplishment

The major standardization projects being pursued by the FGED Society include:

Points of Contact

B.F. Francis Ouellette
Associate Director, Informatics and Biocomputing Program
Ontario Institute for Cancer Research (OICR)
101 College Str. Ste 800
Toronto, Ontario, Canada, M5G 0A3
phone: 416-673-8511
email: francis@oicr.on.ca
http://oic: r.on.ca/person/researcher/francis-ouellette

Sponsors & Partners

An organization may sponsor FGED itself. This includes year-round recognition on the FGED website and discounted sponsorship and vendor booth rates for the annual conference. For more information about society-level sponsorship, contact Ronald Taylor (ronald.taylor24@gmail.com)

There are no fees to join, and memberships are non-voting.

To sign up as a member of FGED, subscribe to one or both of its mailing lists:

  • discuss.fged.org for general discussion about FGED-related topics

  • announce.fged.org for announcements about FGED Society news and events

FGED respects its members’ privacy and will not share, trade, or rent their details with any other organization.


Last Updated: 04/15/2016

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