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ArrayExpress and MAGE Jamboree II

Ugis Sarkans, EBI

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Outline

• what is ArrayExpress

• overall architecture

• status and future

• MAGE Jamboree II

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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

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Classdiagram

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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

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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

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ArrayExpress component architecture

central database(experiment-centred

queries)

data warehouse(gene-centred

queries)

application server(Java servlets)

Web server

image server

ArrayExpress

curation

MAGE-ML

API

submission/curation tool

database

User

MIAMEexpress

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ArrayExpress architecture

ArrayExpress(Oracle)

Browsersubmission/curation tool

database

MIAMEexpress

MAGE-ML(DTD)

MAGE-OM

MAGE-ML (doc)MAGE-ML (doc)MAGE-ML (doc)

dataloader

Velocitytemplateengine

Castor

object/relationalmapping

Web pagetemplateWeb pagetemplate

Java servlets Tomcat

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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

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Queries

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Sample description

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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)

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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)

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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

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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

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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

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MAGEstk components

MAGE-ML

MAGE-RS(database)

MAGE browsing/annotation tools

MAGE API(Perl, Java, C++)

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• 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

Acknowledgements