1. The European Bioinformatics Institute MAGE-OM and ArrayExpress a brief introduction to the database model Helen Parkinson European Bioinformatics Institute Roche, Basel, 17 Feb 2002

2. The European Bioinformatics Institute Outline  what is MAGE-OM  what is ArrayExpress  what language is used for modeling  MAGE-OM structure  ArrayExpress status and future  MAGE future developments

3. The European Bioinformatics Institute MAGE-OM  MicroArray Gene Expression Object Model  Merging of MAML (MicroArray Markup Language) and GEML (Gene Expression Markup Language)  MAGE-ML, dtd available

4. The European Bioinformatics Institute MAGE: brief history  December 2000 - initial submissions of proposals to OMG (Object Management Group): EBI (on behalf of MGED) - MAML Rosetta (on behalf of GEML community) - GEML + some IDLs NetGenics - IDLs  Decision to proceed with a joint submission  Decision to comply with Model Driven Architecture (MDA) principles  October 2001 - joint submission to OMG (Rosetta and MGED)

5. The European Bioinformatics Institute ArrayExpress (2)  implementation - first half of 2001 - Oracle schema, data loader (from MAML), prototype Web interface, a few datasets loaded  decision to use MAGE-OM as basis for further development  EU funding - 2002-2004, 8 new positions

6. The European Bioinformatics Institute ArrayExpress - features  MIAME-compliant  able to import MAML (MAGE-ML) formatted data  can deal with both raw and processed data  independence of: experimental platforms image analysis methods data normalization methods  object model-based query mechanism  supports upcoming OMG standard for expression data

7. The European Bioinformatics Institute Unified Modeling Language  graphical language for describing software systems (and more..)  notation - yes  methodology - no

8. The European Bioinformatics Institute Class diagram

9. The European Bioinformatics Institute Class diagrams - notation  classes  attributes types  operations  relationships subclass relationship aggregate relationship association role names cardinalities navigation

10. The European Bioinformatics Institute class class from another package attribute aggregation navigation role name cardinality association name inheritance

11. The European Bioinformatics Institute Simplest Model Publication External links 6 parts of a microarray experiment www.mged.org HybridisationArray Gene (e.g., EMBL ) Sample Source (e.g., Taxonomy ) Data Experiment Normalisation

12. The European Bioinformatics Institute Class diagram

13. The European Bioinformatics Institute BSANEBQS Description Protocol Measurement Audit Treatment Transformation BioEventExperiment ArrayDesign BioMaterial BioAssayData BioAssay DesignElement UML Packages HigherLevelAnalysis BioSequence ArrayManufacture QuantitationType

14. The European Bioinformatics Institute Top level structure

15. The European Bioinformatics Institute BioAssay

16. The European Bioinformatics Institute Biomaterial

17. The European Bioinformatics Institute BioSequence

18. The European Bioinformatics Institute Protocol

19. The European Bioinformatics Institute AuditAndSecurity

20. The European Bioinformatics Institute Measurement

21. The European Bioinformatics Institute ArrayExpress: current status  Object model (MAGE-OM) - stable  Database schema - generated (standard SQL, Oracle)  Data loader from MAGE-ML format - generated  Web interface (queries, browsing) - under development and test  Data submission tool under development and test (MIAMExpress

22. The European Bioinformatics Institute Near future developments  Data from collaborators  Data uploading and Web interface made public  Data warehousing  Integration with existing tools (Expression Profiler)  New analytical tools  Links with other databases  Data curation

23. The European Bioinformatics Institute Resources  Web site www.mged.org www.sourceforge.net/projects/mged www.ebi.ac.uk/microarray Mailing list lsr-ge@ebi.ac.uk to subscribe, send the following to majordomo@ebi.ac.uk subscribe lsr-ge