1 Update on ArrayExpress & standards Ugis Sarkans, EBI.

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Presentation transcript:

1 Update on ArrayExpress & standards Ugis Sarkans, EBI

2 MAGE-OM MAGE-OM: MicroArray Gene Expression Object Model –in January 2002 became an “adopted” OMG specification –January to August finalization process –in September became an “available” specification –should be set in stone for the next 2 years –thinking about MAGE v2 started user feedback support for other types of functional genomics data more precise handling of data manipulation

3 BioEvent Experiment ArrayDesign BioMaterial BioAssayData BioAssay DesignElement UML Packages of MAGE HigherLevelAnalysis BioSequence Array QuantitationType Description Protocol Measurement AuditAndSecurity BQS what was used what was done results miscellaneous

4 MAGE* MAGE-ML: MicroArray Gene Expression Markup Language –generated from MAGE-OM, therefore evolved automatically – translation from Jan 2002 to Sep 2002 DTD quite easy MAGEstk: MicroArray Gene Expression Software ToolKit –Jamboree IV in Stanford, beginning of December –used in MIAMExpress (MAGE-ML export)

5 MAGEstk 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

6 MAGEstk (cont.) Use opensource/standard modules/packages –Xerces, JDBC, etc. Implementation in Java, C++, Perl, Python database access modules on top of these APIs –Postgres schema –DB access layer annotation tools - planned

7 ArrayExpress: data Currently - 9 experiments, 4 array designs: –from EMBL - human, yeast –from Sanger - pombe Coming: –array descriptions: Affymetrix, Agilent –labs: TIGR, Utrecht, more from Sanger,... –export from existing DBs: SMD, RAD –tools - MAGE-ML export: BASE, maxd,... –ILSI project

8 ArrayExpress (Oracle + Tomcat) Other Microarray databases www EBI Expression Profiler External Bioinformatics databases Data analysis www Queries www MIAMExpress (MySQL) MAGE-ML Submissions Array Manufacturers LIMS Microarray software Data Analysis software ArrayExpress Infrastructure MAGE-ML import, export Local MIAMExpress Installations Data pipelines MAGE-ML

9 Tomcat ArrayExpress architecture ArrayExpress (Oracle) MAGE-ML (DTD) MAGE-OM MAGE-ML (doc) MAGE loader Velocity template engine Castor object/ relational mapping Web page template Web page template Java servlets MAGE validator MAGE unloader error.log

10 Array Design - accession - name Protocol - accession Experiment - accession Organisation - name Array SpeciesSample Hybridisation Experiment Design Experiment Type Experimental Factor Person - last name Protocol Type Queries

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13 Experiment plan display

14 ArrayExpress: other technical details Data matrices - stored in NetCDF format: –binary format for efficient storage of multidimensional array Arrays - stored as ADF spreadsheets (in addition to normal MAGE structures)

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17 ratioabsolute change confidence measure namedesign element type speciessample type bioassay type performer labexper. type array design name platform type provider Properties Data warehouse - for gene- and data-driven queries

18 In development Immediate: –interface efficiency improvements –BioAssays - graphical display –better integration with Expression Profiler Medium-term: –user management non-public data (e.g., for reviewers) –MAGE-ML export Curation tool

19 Microarray Informatics team at EBI Alvis Brazma - group leader ArrayExpress Curation MIAMExpress Ugis Sarkans Gonzalo Garcia Helen Parkinson Mohammadreza Shojatalab Expression Profiler Jaak Vilo Research, students Thomas Schlitt Katja Kivinen Johan Rung Patrick Kemmeren Misha Kapushesky Lev Soinov Koichi Tazaki Anastasia Samsonova Susanna Sansone Philippe Rocca-Serra Ele Holloway Niran Abeyguna- wardena Ahmet Oezcimen Gaurab Mukherjee Sergio Contrino Anjan Sharma Aurora Torrente