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MAGE-OM and ArrayExpress database model

MAGE-OM and ArrayExpress database model. Ugis Sarkans, EBI. Outline. what is MAGE-OM what is ArrayExpress what language is used for modeling MAGE-OM structure ArrayExpress status and future MAGE future developments. MAGE-OM. MicroArray Gene Expression Object Model

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MAGE-OM and ArrayExpress database model

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  1. MAGE-OM and ArrayExpress database model Ugis Sarkans, EBI

  2. 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. MAGE-OM • MicroArray Gene Expression Object Model • also: MAGE-ML (.. Markup Language), MAGE-STK (..Software ToolKit) • Merging of MAML (MicroArray Markup Language) and GEML (Gene Expression Markup Language)

  4. 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. Model Driven Architecture • Platform Independent Model (UML) • most of the time spent on this • Platform Specific Models • XML • UML (refined from PIM) • DTD (generated plus hand modifications) • CORBA (not for MAGE) • UML (refined from PIM) • IDL (hopefully generated) • ….

  6. ArrayExpress • 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

  7. 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

  8. 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

  9. Unified Modeling Language • graphical language for describing software systems (and more ..) • notation - yes • methodology - no

  10. UML diagram types • class • state • collaboration • sequence • ……..

  11. State diagram

  12. Sequence diagram

  13. Collaboration diagram

  14. Classdiagram

  15. Class diagrams - notation • classes • attributes • types • operations • relationships • subclass relationship • aggregate relationship • association • role names • cardinalities • navigation

  16. class attribute aggregation inheritance navigation role name class from another package cardinality association name

  17. Classdiagram

  18. Implementation issues • Java, C++ - “easy” • relational databases • classes - tables • 1:1, 1:N - foreign key • N:M - table • subclass relations • all subclasses in the same table • separate table for superclass and subclasses • XML

  19. Tools • Rational Rose • bad graphical capabilities • forward/reverse engineering • API (VB-based) • open source • ArgoUML

  20. BioEvent Protocol Treatment HigherLevelAnalysis Transformation Experiment BioMaterial BioAssayData BioAssay Audit QuantitationType ArrayManufacture Measurement DesignElement ArrayDesign Description BSANE BQS BioSequence UML Packages

  21. Top level structure

  22. BioAssay

  23. Biomaterial

  24. ArrayDesign

  25. DesignElement

  26. DesignElement

  27. DesignElement mapping

  28. Data

  29. BioSequence

  30. ArrayManufacture

  31. Quantitations

  32. HigherLevelAnalysis

  33. BioEvent

  34. Protocol

  35. Description

  36. AuditAndSecurity

  37. Measurement

  38. 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 (queries, browsing) - under development

  39. Near future developments • Dedicated hardware for ArrayExpress • Good quality data coming from collaborators (annotation tools needed) • Data uploading and Web interface made public

  40. Future developments • Integration with existing tools (Expression Profiler) • New analytical tools • Links with other databases • Data curation, liaison with data providers

  41. ArrayExpress architecture API Web server application server (Java servlets) curation tool database ArrayExpress data warehouse central database (experiment-centred) curation MAGE-ML image server

  42. MAGE schedule • OMG meeting, Dublin, November 12-16 - specification hopefully adopted • Mechanism for incorporating changes and user feedback • MAGE programming jamboree, EBI, December 6-11: API development, parser generation, annotation tools (MAGE STK)

  43. Resources • Web site • links to documents • presentations • UML models • also HTML version and PNG image files of diagrams • http://www.geml.org/omg.htm • Mailing list • lsr-ge@ebi.ac.uk • to subscribe, send the following to majordomo@ebi.ac.uk subscribe lsr-ge <yourEmailAddress>

  44. Acknowledgements • Michael Miller (Rosetta) • Dave Nellesen (Incyte) • Alan Robinson (EBI) • Martin Senger (EBI) • Paul Spellman (Lawrence Berkley Lab) • Jason Stewart (NCGR) • Charles Troup (Agilent) • Doug Bassett (Rosetta) • Alvis Brazma (EBI) • Steve Chervitz (Affymetrix) • Francisco Dela Vega (Applied Biosystems) • Michael Dickson (NetGenics) • David Frankel (IONA) • Scott Markel (NetGenics)

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