What is FGED?
The Functional Genomics Data Society - FGED Society, founded in 1999 as the MGED Society, advocates for open access to genomic data sets and works towards providing concrete solutions to achieve this. Our goal is to assure that investment in functional genomics data generates the maximum public benefit. Our work on defining minimum information specifications for reporting data in functional genomics papers have already enabled large data sets to be used and reused to their greater potential in biological and medical research.
We work with other organisations to develop standards for biological research data quality, annotation and exchange. We facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. We promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis.
Defined FGED standards
- 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 (www.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 organisation.
- 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.
What is Functional Genomics?
Functional genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Unlike genomics andproteomics, functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products. 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.