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MAGE-OM and ArrayExpress database model

Ugis Sarkans, EBI

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Outline

• what is MAGE-OM

• what is ArrayExpress

• what language is used for modeling

• MAGE-OM structure

• ArrayExpress status and future

• MAGE future developments

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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)

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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)

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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)

– ….

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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

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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

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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

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Unified Modeling Language

• graphical language for describing software systems (and more ..)

• notation - yes

• methodology - no

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UML diagram types

• class

• state

• collaboration

• sequence

• ……..

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State diagram

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Sequence diagram

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Collaboration diagram

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Classdiagram

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Class diagrams - notation• classes

• attributes– types

• operations

• relationships– subclass relationship– aggregate relationship– association

• role names

• cardinalities

• navigation

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class

class fromanother package

attribute

aggregation

navigation

role name

cardinality

associationname

inheritance

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Classdiagram

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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

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Tools

• Rational Rose– bad graphical capabilities– forward/reverse engineering– API (VB-based)

• open source– ArgoUML

20BSANE BQS

Description

Protocol

Measurement

Audit

Treatment

Transformation

BioEvent

Experiment

ArrayDesign

BioMaterial

BioAssayData BioAssay

DesignElement

UML Packages

HigherLevelAnalysis

BioSequence

ArrayManufactureQuantitationType

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Top level structure

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BioAssay

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Biomaterial

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ArrayDesign

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DesignElement

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DesignElement

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DesignElement mapping

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Data

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BioSequence

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ArrayManufacture

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Quantitations

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HigherLevelAnalysis

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BioEvent

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Protocol

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Description

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AuditAndSecurity

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Measurement

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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 (queries, browsing) - under development

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Near future developments

• Dedicated hardware for ArrayExpress

• Good quality data coming from collaborators (annotation tools needed)

• Data uploading and Web interface made public

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Future developments

• Integration with existing tools (Expression Profiler)

• New analytical tools

• Links with other databases

• Data curation, liaison with data providers

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ArrayExpress architecture

central database(experiment-centred)

data warehouse

application server(Java servlets)

Web server

image server

ArrayExpress

curation

MAGE-ML

API

curation tooldatabase

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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)

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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>

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• Doug Bassett (Rosetta)

• Alvis Brazma (EBI)

• Steve Chervitz (Affymetrix)

• Francisco Dela Vega (Applied Biosystems)

• Michael Dickson (NetGenics)

• David Frankel (IONA)

• Scott Markel (NetGenics)

• Michael Miller (Rosetta)

• Dave Nellesen (Incyte)

• Alan Robinson (EBI)

• Martin Senger (EBI)

• Paul Spellman (Lawrence Berkley Lab)

• Jason Stewart (NCGR)

• Charles Troup (Agilent)

Acknowledgements