1 ArrayExpress Ugis Sarkans, EBI. 2 Overview Underlying standards –MIAME –MAGE* Data submission Data access –annotations –actual data –array design descriptions.

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Presentation transcript:

1 ArrayExpress Ugis Sarkans, EBI

2 Overview Underlying standards –MIAME –MAGE* Data submission Data access –annotations –actual data –array design descriptions Some technical details Future developments

3 What information should be exchanged? MIAME - Minimum Information About a Microarray Experiment –informal specification –paper published in Nature Genetics –goal - to initiate discussion: which details are important and which may not be –ArrayExpress can store MIAME data (and more)

4 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

5 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

6 MAGE-ML MAGE-ML: MicroArray Gene Expression Markup Language –generated from MAGE-OM, therefore evolved automatically – translation from Jan 2002 to Sep 2002 DTD quite easy

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: Jexpress, BASE,... –ILSI project journal requirements: Nature, Lancet,...

8 Help with MAGE-ML: MAGEstk MAGE-ML - the only way of getting data into ArrayExpress MAGEstk: MicroArray Gene Expression Software ToolKit –Jamboree IV in Stanford, beginning of December –used in MIAMExpress (MAGE-ML export)

9 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

10 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

11 ArrayExpress data retrieval main objective - help in finding and initial exploration of data; download for detailed analysis data repository (now) + data warehouse (in development)

12 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 - logical structure

13 Query form

14 Annotation browsing

15 Data representation spots measurements BioAssays (hybridizations, data transformations) QuantitationTypes (signal intensity, ratio etc.) DesignElements (spots, genes) in MAGE/ArrayExpress in Expression Profiler

16 Exporting data to Expression Profiler BioAssays (hybridizations, data transformations) QuantitationTypes (signal intensity, ratio etc.) DesignElements (spots) BioAssayData1 BioAssayData2 select BioAssayData cubes select QuantitationTypes select BioAssays DesignElements (QT,BA) pairs

17 Data export form

18 Array representation - ADF format

19 Experiment plan display

20 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

21 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

22 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)

23 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

24 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 namebiological entity type

25 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