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ArrayExpress and MAGE Jamboree II

ArrayExpress and MAGE Jamboree II. Ugis Sarkans, EBI. Outline. what is ArrayExpress overall architecture status and future MAGE Jamboree II. ArrayExpress. EBI’s public gene expression data repository

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ArrayExpress and MAGE Jamboree II

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  1. ArrayExpress and MAGE Jamboree II Ugis Sarkans, EBI

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

  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. Classdiagram

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

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

  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. Queries

  11. Sample description

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

  18. Acknowledgements • 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

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