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An international meeting on Microarray Gene Expression Databases - MGED1

November 14-15, 1999
European Bioinformatics Institute,
Wellcome Trust Genome Campus, UK

November 14, 1999

10:00-11:00

Arrival, registration

11:00-12:30

Welcome Address

Existing microarray expression database efforts and projects:

12:30-13:30

Lunch

13:30-16:00

  • National Cancer Institute (Ron Taylor)
  • DDBJ (Yoshio Tateno)
  • Sanger Centre (Tom Freeman)
  • National Center for Genome Resources (Harry Mangalam, Bruno Sobral)
  • Affymetrix (John Sowatsky)
  • Gene Logic (Victor Markowitz)
  • Incyte (Julie Klemm) [presentation]

16:00-16:30

Coffee

16:30-17:00

  • EMBL-EBI and DKFZ (Alvis Brazma, Alan Robinson, Martin Vingron) [presentation]

17:00-19:00

Thematic discussion (see preliminary list of topics next page)

19:00-22:30

Buffet dinner (Duxford Lodge, departure by a bus in front of the conference hall)

November 15, 1999

08:30-10:30

Thematic discussion continues

10:30-11:00

Coffee

11:30-12:30

Thematic discussion continues

12:30-13:30

Lunch

13:30-14:15

Founding and sign-up for working-groups

15:00-15:30

Conclusion and departure

Preliminary list of discussion topics
(Please see also the draft recommendations)

  1. What (minimum) information has to be stored about a microarray experiment regarding
    1. expression measurement (image, image analysis output, thumb-nail image, one scalar?)
    2. array
    3. each probe on the array
    4. target source
    5. how to describe and annotate an experiment:
      • sample preparation and treatment (possibly repeated in time-course)
      • hybridisation extract preparation (are there a limited number of standard procedures?)
      • hybridisation procedure
      • scanning
      • image analysis and quantitation
      • experiment as a whole (i.e., set of related hybridisations)
  2. Data storage and communication standards
    1. controlled vocabularies (for source, array, etc)
    2. standard protocols (for hybridisation extract preparation, hybridisation, scanning, etc)
    3. data communication standards (XML?)
  3. Overall database design
    1. can all platforms be accommodated by the same basic data model?
    2. experiment information separated from the array information
    3. reuse of earlier submitted objects in the database
  4. Database population and data submission
    1. XML based flat-file format (for experiment and arrays)
    2. how to begin (what cooperation can be expected from labs at the beginning)?
    3. how detailed information is it realistic to expect?
    4. how to encourage data submissions?
    5. how many experiments per month during the first year we can expect?
    6. what are the most convenient submission procedure for labs (XML flat files, Web form, direct output from LIMS)?
    7. quality control at early stage
  5. Data normalisation and cross-platform comparison
    1. are there experiments on the public domain comparing different platforms for designing cross-platform normalisation procedures
    2. is it realistic that the community can agree on common controls for the experiments?
  6. Data curation policy
    1. can the data quality be policed?
    2. can mechanisms be designed to remove or flag experiments (spots) that later have been confirmed to be inaccurate?
    3. how much power should curators have?
    4. third party annotations?
    5. can formal, quantifiable experiment quality assessment indicators be designed (e.g., the number of replicates, quality assessment of the spots on the array, etc)
  7. List of interesting queries and data mining problems that have to be supported by the database.
  8. Various database initiatives and collaboration possibilities

 

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