1. 1 ArrayExpress and MAGE Jamboree II Ugis Sarkans, EBI

2. 2 Outline what is ArrayExpress overall architecture status and future MAGE Jamboree II

3. 3 ArrayExpress EBI’s public gene expression data repository first version (object model) - 1999, in collaboration with German Cancer Research Centre (DKFZ) second version (object model) - end of 2000, prototype development funded by Incyte

4. 4 Class diagram

5. 5 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 www.ebi.ac.uk/arrayexpress

6. 6 ArrayExpress - features MIAME-compliant able to import MAGE-ML formatted data can deal with: –raw data –processed data –data transformations independence of: –experimental platforms –image analysis methods –data normalization methods object model-based query mechanism

7. 7 ArrayExpress component architecture central database (experiment-centred queries) data warehouse (gene-centred queries) application server (Java servlets) Web server image server ArrayExpress curation MAGE-ML API submission/ curation tool database User MIAMEexpress

8. 8 ArrayExpress architecture ArrayExpress (Oracle) Browser submission/ curation tool database MIAMEexpress MAGE-ML (DTD) MAGE-OM MAGE-ML (doc) data loader Velocity template engine Castor object/ relational mapping Web page template Web page template Java servlets Tomcat

9. 9 ArrayExpress: current status Object model (MAGE-OM) - stable Database schema - generated (standard SQL, we run under Oracle) Data loader from MAGE-ML - generated Web interface - under development: –queries: by experiment by array by sample –browsing

10. 10 Queries

11. 11 Sample description

12. 12 Near future developments Dedicated hardware for ArrayExpress Good quality data coming from collaborators: –annotation tools essential (MIAMEexpress) Data uploading and Web interface made public interface with analysis tools (Expression Profiler)

13. 13 Future developments Integration with other analysis tools New visualization methods and tools New analytical tools Links with other databases Data curation, liaison with data providers –development of standard ontologies Data warehouse (gene-oriented queries)

14. 14 MAGE Jamboree II open-source implementation efforts: –MAGE Jamboree I, Toronto, September 13-19, sponsored by Iobion –Jamboree II at EBI, December 6-11 objective: bring MAGE to life

15. 15 Programming APIs Mapping of MAGE-OM to language-specific OMs API’s are automatically generated from the OM specifications –Get/set methods for associations –Get/set methods for attributes XML language-specific OM marshallers/unmarshallers - also automatically generated

16. 16 Programming APIs (cont.) Use standard modules/packages –Xerces, JDBC, etc. Implementation in Java, C++, Perl Building annotation tools/database access modules on top of these APIs

17. 17 MAGEstk components MAGE-ML MAGE-RS (database) MAGE browsing/ annotation tools MAGE API (Perl, Java, C++)

18. 18 EBI microarray team/database department: –Alvis Brazma (team leader) –Helen Parkinson (curation, MIAMExpress) –Mohammad Shojatalab (MIAMExpress) –Jaak Vilo (Expression Profiler) –Ahmet Oezcimen (Oracle DBA) –Susanna Sansone (curation, MIAMExpress) MAGE developers: –MGED –Rosetta Biosoftware Acknowledgements