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Home : Meetings : MGED1 : Agenda
An international meeting on Microarray Gene Expression Databases - MGED1
November 14-15, 1999
European Bioinformatics Institute,
Wellcome Trust Genome Campus, UK
November 14, 1999
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10:00-11:00 |
Arrival, registration |
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11:00-12:30 |
Welcome Address
Existing microarray expression database efforts and projects:
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12:30-13:30 |
Lunch |
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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] |
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16:00-16:30 |
Coffee |
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16:30-17:00 |
- EMBL-EBI and DKFZ (Alvis Brazma, Alan Robinson, Martin Vingron)
[presentation] |
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17:00-19:00 |
Thematic discussion (see preliminary list of topics next page) |
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19:00-22:30 |
Buffet dinner (Duxford Lodge, departure by a bus in front of the conference hall) |
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November 15, 1999
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08:30-10:30 |
Thematic discussion continues |
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10:30-11:00 |
Coffee |
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11:30-12:30 |
Thematic discussion continues |
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12:30-13:30 |
Lunch |
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13:30-14:15 |
Founding and sign-up for working-groups |
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15:00-15:30 |
Conclusion and departure |
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Preliminary list of discussion topics
(Please see also the draft recommendations)
- What (minimum) information has to be stored about a microarray experiment regarding
- expression measurement (image, image analysis output, thumb-nail image, one scalar?)
- array
- each probe on the array
- target source
- 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)
- Data storage and communication standards
- controlled vocabularies (for source, array, etc)
- standard protocols (for hybridisation extract preparation, hybridisation, scanning, etc)
- data communication standards (XML?)
- Overall database design
- can all platforms be accommodated by the same basic data model?
- experiment information separated from the array information
- reuse of earlier submitted objects in the database
- Database population and data submission
- XML based flat-file format (for experiment and arrays)
- how to begin (what cooperation can be expected from labs at the beginning)?
- how detailed information is it realistic to expect?
- how to encourage data submissions?
- how many experiments per month during the first year we can expect?
- what are the most convenient submission procedure for labs (XML flat files, Web form, direct output from LIMS)?
- quality control at early stage
- Data normalisation and cross-platform comparison
- are there experiments on the public domain comparing different platforms for designing cross-platform normalisation procedures
- is it realistic that the community can agree on common controls for the experiments?
- Data curation policy
- can the data quality be policed?
- can mechanisms be designed to remove or flag experiments (spots) that later have been confirmed to be inaccurate?
- how much power should curators have?
- third party annotations?
- can formal, quantifiable experiment quality assessment indicators be designed (e.g., the number of replicates, quality assessment of the spots on the array, etc)
- List of interesting queries and data mining problems that have to be supported by the database.
- Various database initiatives and collaboration possibilities
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