the european bioinformatics institute mage-om and arrayexpress a brief introduction to the database...
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The European Bioinformatics InstituteThe European Bioinformatics Institute
MAGE-OM and ArrayExpress a brief introduction to the
database model
Helen Parkinson
European Bioinformatics Institute
Roche, Basel, 17 Feb 2002
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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
Merging of MAML (MicroArray Markup Language) and GEML (Gene Expression Markup Language) MAGE-ML, dtd available
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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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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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Classdiagram
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Class diagrams - notation classes attributes
types operations relationships
subclass relationship
aggregate relationship
associationrole names
cardinalities
navigation
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class
class fromanother package
attribute
aggregation
navigation
role name
cardinality
associationname
inheritance
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Simplest Model
PublicationExternal links
6 parts of a microarray experiment
www.mged.org
Hybridisation ArrayGene
(e.g., EMBL)Sample
Source(e.g., Taxonomy)
Data
Experiment
Normalisation
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Classdiagram
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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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BioSequence
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Protocol
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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, Oracle) Data loader from MAGE-ML format -
generated Web interface (queries, browsing) -
under development and test Data submission tool under
development and test (MIAMExpress
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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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Resources Web site
www.mged.org
www.sourceforge.net/projects/mged
www.ebi.ac.uk/microarray
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