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

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

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

The European Bioinformatics Institute MAGE: brief history  December 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 joint submission to OMG (Rosetta and MGED)

The European Bioinformatics Institute ArrayExpress (2)  implementation - first half of 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 , 8 new positions

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

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

The European Bioinformatics Institute Class diagram

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

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

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

The European Bioinformatics Institute Class diagram

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

The European Bioinformatics Institute Top level structure

The European Bioinformatics Institute BioAssay

The European Bioinformatics Institute Biomaterial

The European Bioinformatics Institute BioSequence

The European Bioinformatics Institute Protocol

The European Bioinformatics Institute AuditAndSecurity

The European Bioinformatics Institute Measurement

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

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

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