FGED Society

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FGED Society
Mged logo.png
Abbreviation FGED
Formation 1999
Type NPO
Purpose Scientific
Official language
English
President
John Quackenbush
Main organ
Board of directors
Website fged.org

The Functional GEnomics Data (FGED) Society (formerly known as the MGED Society) is a non-profit, volunteer-run international organization of biologists, computer scientists, and data analysts that aims to facilitate biological and biomedical discovery through data integration. The approach of FGED is to promote the sharing of basic research data generated primarily via high-throughput technologies that generate large data sets within the domain of functional genomics.

Members of the FGED Society work to establish standards for data quality, management, annotation and exchange; facilitate the creation of software tools that leverage these standards; and work with other standards organizations and promoting the sharing of high quality, well annotated data within the life sciences and biomedical communities.

Founded in 1999 as the "Microarray Gene Expression Data (MGED) Society," this organization changed its name to the "Functional Genomics Data Society" in 2010 to reflect the fact that it has 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 includes data generated using any functional genomics technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

History[edit]

The FGED Society was formed in 1999 at a meeting on Microarray Gene Expression Databases in recognition of the need to establish standards for sharing and storing data from DNA microarray experiments. Originally named the "MGED Society," the society began with a focus on DNA microarrays and gene expression data.

The original MGED Society was incorporated in 2002 as a non-profit public benefit organization with the title Microarray Gene Expression Data Society and obtained permanent charity status in 2007. The MGED name was legally changed in 2007 to Microarray and Gene Expression Data Society to emphasize a broader scope.

In September 2008, the Society decided to promote itself simply as the MGED Society to broaden the Society's scope beyond microarray technology and gene expression applications, yet still retain the recognized value of the MGED name within the community.

In July 2010, the society voted to change its name to the "Functional Genomics Data (FGED) Society" to reflect its current mission which goes beyond microarrays and gene expression to encompass data generated using any functional genomics technology applied to genomic-scale studies of gene expression, binding, modification (such as DNA methylation), and other related applications. This was formally announced on 14 July 2010 at the society's "MGED13" annual meeting.[1]

Membership[edit]

The FGED Board of Directors and Advisory Board consist of volunteers from academia, industry, government, and journals representing a cross-section of those generating, analyzing, archiving, and publishing in the functional genomics area. Although there is no formal membership, the attendees of the annual FGED meetings are considered to be part of the FGED community.

Achievements[edit]

To date, FGED has produced a variety of standards specifications pertaining to DNA microarray experiments. These standards are designed to improve the annotation, communication, and sharing of data and findings from such experiments within the life science research community.

MINSEQE[edit]

Minimal Information about a high-throughput SEQuencing Experiment (MINSEQE) is a data content standard that describes what information is needed to adequately document a high-throughput sequencing experiments for the purpose of interpretation and replication of the results.[2]

MIAME[edit]

MIAME (Minimal Information About a Microarray Experiment) is a data content standard that describes what information is needed to adequately document a DNA microarray experiment for the purpose of interpretation and replication of the results.

MAGE-OM and MAGE-TAB[edit]

MAGE-OM (MicroArray Gene Expression Object Model) is a data exchange and data modeling standard for use in encoding data from microarray experiments for the purpose of export and import into software tools and databases via XML files. MAGE-OM is a platform-independent model implemented in the XML-based MAGE-ML format.

A new version, MAGE-TAB, has been developed to be easier to understand and generate by data producers as it is in a format (tab-delimited) that can be viewed and edited using widely available spreadsheet software, such as Microsoft Excel.[3]

MGED Ontology[edit]

The MGED Ontology (MO) provides a standard terminology for describing components of a DNA microarray experiment.[4] The Ontology for Biomedical Investigations (OBI) is being developed as a replacement for the MO. A mapping of ontology terms from MO to OBI is available.[5]

Annual meeting[edit]

A major component of the FGED Society effort has been the annual FGED meeting to showcase cutting edge scientific work and promote standards.[6]

The FGED Society has held its annual meeting at venues around the world since 1999, coordinating with a local scientific organization that provides space for talks, poster sessions, workshops, and tutorials.

Information about the current year's meeting is accessible at FGEDmeeting.org.

External links[edit]

See also[edit]

References[edit]

  1. ^ FGED_Society. "Big news: MGED has a new name: FGED - Functional Genomics Data Society". Twitter. Retrieved 10 August 2010. 
  2. ^ Functional Genomics Data Society (June 2012). "Minimum Information about a high-throughput SEQuencing Experiment". 
  3. ^ "MAGE-TAB Homepage". FGED Website. Retrieved 2012-07-31. 
  4. ^ "The MGED Ontology FAQ". MO project website. Retrieved 2008-11-23. 
  5. ^ "Mapping terms between MO and Ontology for Biomedical Investigations". MGED Ontology Working Group. Retrieved 10 August 2010. 
  6. ^ "List of FGED annual meetings". FGED website. Retrieved 2013-04-02.