FGED History

About FGED and its mission

The Functional Genomics Data Society - FGED Society was a non-profit, volunteer-run international organization of biologists, computer scientists, and data analysts that advocated for reproducible research and open access to genomic data sets and worked towards providing concrete solutions to achieve those goals. It began in 1999 as a grass-roots effort, became a 501(c)3 non-profit that hosted annual meetings through 2013, and eventually wound down its operations by 2021.

FGED's goal was to assure that investment in functional genomics data generates the maximum public benefit. Its ground-breaking work on defining minimum information specifications for reporting data in functional genomics papers enabled large data sets to be used and reused to their greater potential in biological and medical research.

FGED worked with other organizations to accelerate and support the effective sharing and reproducibility of functional genomics data. The Society facilitated the creation and use of standards and software tools that allowed researchers to annotate and share their data easily. It promoted scientific discovery driven by genome wide and other biological research data integration and meta-analysis.


The Society was founded in 1999 as the "Microarray Gene Expression Data (MGED) Society" then changed its name to the "Functional GEnomics Data (FGED) Society" in 2010 to reflect the fact that it had broadened its focus beyond the application of DNA microarrays for gene expression analysis to include technologies such as high-throughput sequencing. The scope of the FGED Society included data generated using any functional genomics technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

FGED website, circa 2010
FGED website, circa 2015

What is Functional Genomics?

Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing). Functional genomics focuses on the dynamic aspects such as gene transcription, translation, regulation of gene expression and proteinā€“protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. A key characteristic of functional genomics studies is their genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional "gene-by-gene" approach.

Source: https://en.wikipedia.org/wiki/Functional_genomics

Historical Highlights

  • November 1999 - MGED was founded as a grass roots 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 home-page (originally mged.org) and e-mail 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 non-profit organization.

  • October 2002 - Several major scientific journals, including the Nature group, The Lancet, Cell and EMBO journal 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, The University of Pennsylvania etc.

  • Jan 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 towards data standards and more open data sharing by publishing multiple papers on the importance thereof. Today, data sharing is standard policy for many journals and is required of most obtaining NIH funding.

  • Sept. 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 microrarray 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).

  • Oct 2009: Initiated a community service to facilitate data deposition.

  • 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.

  • June 2013 - The FGED Society hosted its final conference, convening in Seattle, WA.

  • January 2021 - FGED paper assessing compliance with MIAME and MINSEQE guidelines in transcriptome research was published in bioRxiv.

  • September 2021 - The FGED Society finalized its shut down as an organization.

Board Members of the FGED Society

The FGED Society board of directors came from a variety of organizations, universities, and companies, and served on a volunteer basis or were supported in their FGED-related efforts through a government grant which ended in 2010. The last serving members of the FGED board and their affiliations at the time are listed here, with previous board members included below.


B.F. Francis Ouellette (President), Ontario Institute for Cancer Research, University of Toronto

Ronald Taylor (Treasurer), Pacific Northwest National Laboratory (US Dept of Energy)

Steve Chervitz Trutane (Secretary), Personalis, Inc.

Other Board members:

Alvis Brazma, EMBL-EBI

Roger Bumgarner, University of Washington

Cesare Furlanello, Kessler Foundation

Michael Miller, Institute for Systems Biology

John Quackenbush, Harvard University

Michael Reich, Broad Institute

Chris Stoeckert, University of Pennsylvania

Brian Wilhelm, University of Montreal

Past Board Members:

Catherine Ball, Stanford University

Helen Parkinson, EMBL-EBI

Gabriella Rustici, EMBL-EBI

Gavin Sherlock, Stanford University

Jennifer Weller, University of North Carolina