Mission

What is MGED?

The MGED Society is an international organization of biologists, computer scientists, and data analysts that aims to facilitate biological and biomedical discovery through data integration. Our approach is to promote the sharing of large data sets generated by high throughput functional genomics technologies. Historically, MGED began with a focus on microarrays and gene expression data. However, the scope of MGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

Members of MGED work to establish standards for data quality, management, annotation and exchange; facilitate the creation of 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.

Defined MGED standards

Historical highlights of the MGED society

  • 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.

MGED meetings

MGED organises meetings to provide an opportunity for members to meet face-to-face, to communicate their progress to others, to establish goals and priorities, and to educate the scientific community at large. Since MGED 2, these meetings have been major conferences, with several hundred participants, drawn from a truly international audience.

List of meetings are available from here.

MGED supported meetings

Some meetings, while not organised by MGED, have such large impact on the MGED goals and projects that they are of special importance to the organisation.

SOFG - Standards and Ontologies for Functional Genomics, Cambridge UK, November 2002 (EBI, sponsored jointly by the Wellcome Trust and NIH)

MGED/AAAS - 'Microarrays and Functional Genomics', Denver, USA, February 2003

More recent supported meetings are available from here.

MGED programming jamborees

Programmers from around the world meet at MGED programming jamborees to learn about the MAGE-OM, MAGE-ML and MAGEstk. For a few days, they work collaboratively on a discrete set of programming tasks that are valuable to the MGED project as a whole. In addition the first day of the meeting comprises a tutorial, to educate users about MIAME and MAGE, and solicit feedback from them.

  • 1st Jamboree - September 2001 - Toronto, Canada
  • 2nd Jamboree -  December 2001 - Cambridge, England
  • 3rd Jamboree - May 2002 - Seattle, WA, USA
  • 4th Jamboree - December 2002 - Stanford, CA, USA

More recent programming jamborees are available from here.

MGED Goals

  1. To promote the adoption of MIAME and MAGE standards by the microarray community.  This includes adoption by scientific journals and public funding agencies, as well as by microarray software and hardware vendors and users.
  2. To assist in the development of both commercial and free MIAME- and MAGE-compatible software, including microarray LIMS, laboratory databases, data analysis tools and public repositories for microarray data.  This is being accomplished by participation in open-source software development, offering tutorials, lectures, and consultation, as well as facilitating collaboration among participating companies and members of the academic community.
  3. To develop microarray data quality standards by promoting the sharing and standardisation of experimental and data transformation (normalisation) protocols, and adoption of best practices and the creation of standards for data quality metrics.
  4. To facilitate the development and adoption of standards (ontologies and controlled vocabularies) for describing high-throughput life sciences experiments and microarray experiments in particular. As part of this goal we are participating in the community development of ontologies and support the Global Open Biological Ontologies (GoBo) effort. GoBo ontologies are exchangeable in a standard format and open for use without constraint.
  5. To continue the development of the MIAME and MAGE standards to include other types of microarray experiments (in addition to gene expression), as well as other genomics and proteomics technology based experiments. Specific short term tasks:
    1. Maintaining and developing the MGED home page, which promotes the MGED goals ( www.mged.org).
    2. Lobbying journals and funding agencies for adoption of the MIAME recommendations, and gathering and analysing the feedback from journals, reviewers and authors.
    3. Organising and participating in conferences relevant to MGED goals:
      SOFG, MGED/AAAS, MGED 6 (France).
    4. Offering presentations and tutorials promoting MGED goals in conferences and workshops.
    5. Maintaining a set of MGED presentations on the MGED home page.

The MGED Working Groups

To help accomplish its goals, the MGED society created four working groups early in its existence, each focusing on particular tasks. The working groups, and their goals are described below:

The MIAME Working Group

The MIAME working group is focused explicitly on the development of the MIAME document that describes the data that should be communicated to allow others to fully understand and utilise microarray data. The MIAME working group has the following goals:

  1. To discuss, promote and improve the MIAME document by involving the scientific community via the mailing list, publication in peer-reviewed journals, and oral and poster presentations at relevant scientific conferences.
  2. To develop criteria for the certification of software tools as being 'MIAME supportive', and to maintain a list of such tools.
  3. To extend MIAME to include other, non-expression, microarray experiments, including ChIP on Chip and array CGH experiments.

The MAGE Working Group

The MAGE working group is focused on further development of the MAGE Object model, its integration with other projects, and education of developers and users about the model. In this way, the working group hopes to make MAGE a more compelling platform, as we work towards version 2 of MAGE, for which we intend to seek funding. Specific goals are:

  1. To identify which packages within the Object Model can be reused in other functional genomics domains.  Many of the packages in MAGE are not restricted to microarray gene expression experiments, but instead could be generalised to other types of high throughput experiments, such as proteomic experiments.  The latter will likely be done in collaboration with HUPO.
  2. To support more advanced analysis methods within the Object Model (e.g. promoter searches, functional annotation etc.).
  3. To rework the BioMaterial and BioEvent packages.  While the current versions are sufficient for the majority of our current needs, we need to make them more robust and flexible, in part by incorporation of such things as real-life behaviours.
  4. To greatly improve the documentation associated with the Object Model, including the creation of a comprehensive set of well-written use cases.  It has been clear that many groups adopting MAGE have found the lack of use cases to be somewhat of a hurdle to its adoption, a situation which we would like to rectify.
  5. To write a book on MAGE and MAGE-stk.  This is currently in the planning stages, with the O'Reilly publisher, and would greatly help the adoption of MAGE.
  6. To incorporate the current MGED Ontology into MAGE.
  7. To switch over from using a DTD to using XML Schema. This will then allow MAGE providers to easily support web services via the BioMOBY project.
  8. To create new independent small ontologies for the attributes of objects within the model that need them in cooperation with the Ontology Working Group.

The Ontology Working Group (OWG)

The Ontology working group is focused on providing controlled vocabularies, both structured ones and simple enumerated lists, that can be used to annotate attributes of microarray experiments. The current goals include:

  1. To finish covering the entire set of attributes of a microarray experiment in cooperation with the MAGE Working Group.
  2. To provide instances for all the concepts that can be used in user-fillable forms, especially those that can be used as identifiers.
  3. To standardise the usage of the ontologies in annotation forms.
  4. To develop and maintain a list of available ontologies that can be used for sample description (anatomy, development, etc.), preferably with recommendations of ontologies that are appropriate to specific situations.

The Data Transformation and Normalisation Working Group

The Data Transformation and Normalisation working group is focused on the issues of how measured data from a microarray experiment are subsequently manipulated, and how their quality can be assessed.

  1. To standardise the recording of data transformation.  This goal is not to say that everyone should transform or normalise their data in the same way, but instead that they should record and communicate how they normalise or transform their data in an common, unambiguous manner. This requires the creation of ontologies to annotate the types of data processing steps, as well as interfacing with MAGE, to be able to record such steps within a MAGE-ML document.
  2. To develop metrics that are practical for use in assessing the quality of microarray data.  Part of the task will be to develop local, per-feature metrics, to indicate whether a particular feature's data is useful. The other part of the task will be the development of global metrics that indicate whether an array as a whole is of a good quality.  We will develop metrics for both two-color spotted arrays, as well as Affymetrix-style oligonucleotide arrays.
  3. To create and provide documentation on data transformation and analysis methods, and to educate end-users.  This will be done via our website, and by tutorials at relevant scientific meetings.

The Reporting Structure for Biological Investigations Working Groups (RSBI WGs)

The Reporting Structure for Biological Investigations Working Groups (RSBI WGs) is enlarging objectives and restructuring activities to include other communities, where efforts are already underway to promote standardization and develop databases to facilitate data exchange.

The group recognizes the need for a ‘single point of focus' for new domains and recommends the formation of a new working group to include Toxicogenomics, Nutrigenomics and Environmental Genomics domains of application.

 

Relevant Publications

This section has now moved to here.  

MGED Sponsors