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The Functional GEnomics Data Society (FGED) (formerly known as the MGED Society) was 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 was to promote the sharing of
basic research Basic research, also called pure research or fundamental research, is a type of scientific research with the aim of improving scientific theories for better understanding and prediction of natural or other phenomena. In contrast, applied rese ...
data generated primarily via high-throughput technologies that generate large data sets within the domain of
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 ...
. Members of the FGED Society worked with other organizations to support the effective sharing and reproducibility of functional genomics data; facilitate the creation of standards and software tools that leverage the standards; and promote 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 A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to g ...
for gene expression analysis to include technologies such as
high-throughput sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
. 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. In September 2021, the FGED Society ceased operations.


History

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 A nonprofit organization (NPO) or non-profit organisation, also known as a non-business entity, not-for-profit organization, or nonprofit institution, is a legal entity organized and operated for a collective, public or social benefit, in co ...
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 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 ...
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.


Presidents of the FGED Society

Board members and officers of the FGED Society are elected annually each May and start serving in June. Presidents of the FGED Society along with their terms in office are as follows: * Francis Ouellette (2013–2021) * John Quackenbush (2011–2013) * Chris Stoeckert (2007–2011) * Catherine Ball (2003–2007) * Alvis Brasma (1999–2003)


Membership

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.


Standards

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

Minimal Information about a high-throughput SEQuencing Experiment (MINSEQE) is a data content minimum information standard that describes the essential information needed to adequately document a
high-throughput sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
experiment for the purpose of interpretation and replication of the results.


MIAME

MIAME Minimum information about a microarray experiment (MIAME) is a standard created by the FGED Society for reporting microarray experiments. MIAME is intended to specify all the information necessary to interpret the results of the experiment unam ...
(Minimal Information About a Microarray Experiment) is a data content standard that describes the essential information needed to adequately document a DNA microarray experiment for the purpose of interpretation and replication of the results. It was the first published example of a minimum information standard for high-throughput experiments in the life sciences, and as such, laid the groundwork for similar standards in other bioscience domains.


MAGE-OM and MAGE-TAB

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 Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable ...
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 Microsoft Excel is a spreadsheet developed by Microsoft for Windows, macOS, Android and iOS. It features calculation or computation capabilities, graphing tools, pivot tables, and a macro programming language called Visual Basic for App ...
.


MGED Ontology

The MGED Ontology (MO) provides a standard terminology for describing components of a DNA microarray experiment. The
Ontology for Biomedical Investigations The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, ...
(OBI) is being developed as a replacement for the MO. A mapping of ontology terms from MO to OBI is available.


Annual meeting

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


Past meetings of the FGED Society

Here is a list of the annual meeting dates and locations for past meetings of the FGED Society. All meetings from 2010 and prior were held under the name "MGED Society".


See also

*
Minimum Information Standards Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the ...
*
Genomic Standards Consortium The Genomic Standards Consortium (GSC) is an initiative working towards richer descriptions of our collection of genomes, metagenomes and marker genes. Established in September 2005, this international community includes representatives from a ran ...


References

{{DEFAULTSORT:Fged Society Bioinformatics organizations Genomics organizations International scientific organizations