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MAGE-OM and ArrayExpress database model. Ugis Sarkans, EBI. Outline. what is MAGE-OM what is ArrayExpress what language is used for modeling MAGE-OM structure ArrayExpress status and future MAGE future developments. MAGE-OM. MicroArray Gene Expression Object Model

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Outline
Outline

  • what is MAGE-OM

  • what is ArrayExpress

  • what language is used for modeling

  • MAGE-OM structure

  • ArrayExpress status and future

  • MAGE future developments


Mage om
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)


Mage brief history
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)


Model driven architecture
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)

    • ….


Arrayexpress
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


Arrayexpress 2
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


Arrayexpress features
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


Unified modeling language
Unified Modeling Language

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

  • notation - yes

  • methodology - no


Uml diagram types
UML diagram types

  • class

  • state

  • collaboration

  • sequence

  • ……..





Class diagram
Classdiagram


Class diagrams notation
Class diagrams - notation

  • classes

  • attributes

    • types

  • operations

  • relationships

    • subclass relationship

    • aggregate relationship

    • association

      • role names

      • cardinalities

      • navigation


Mage om and arrayexpress database model

class

attribute

aggregation

inheritance

navigation

role name

class from

another package

cardinality

association

name


Class diagram1
Classdiagram


Implementation issues
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


Tools
Tools

  • Rational Rose

    • bad graphical capabilities

    • forward/reverse engineering

    • API (VB-based)

  • open source

    • ArgoUML


Uml packages

BioEvent

Protocol

Treatment

HigherLevelAnalysis

Transformation

Experiment

BioMaterial

BioAssayData

BioAssay

Audit

QuantitationType

ArrayManufacture

Measurement

DesignElement

ArrayDesign

Description

BSANE

BQS

BioSequence

UML Packages



















Arrayexpress current status
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


Near future developments
Near future developments

  • Dedicated hardware for ArrayExpress

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

  • Data uploading and Web interface made public


Future developments
Future developments

  • Integration with existing tools (Expression Profiler)

  • New analytical tools

  • Links with other databases

  • Data curation, liaison with data providers


Arrayexpress architecture
ArrayExpress architecture

API

Web server

application server

(Java servlets)

curation tool

database

ArrayExpress

data warehouse

central database

(experiment-centred)

curation

MAGE-ML

image server


Mage schedule
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)


Resources
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>


Mage om and arrayexpress database model

Acknowledgements

  • Michael Miller (Rosetta)

  • Dave Nellesen (Incyte)

  • Alan Robinson (EBI)

  • Martin Senger (EBI)

  • Paul Spellman (Lawrence Berkley Lab)

  • Jason Stewart (NCGR)

  • Charles Troup (Agilent)

  • Doug Bassett (Rosetta)

  • Alvis Brazma (EBI)

  • Steve Chervitz (Affymetrix)

  • Francisco Dela Vega (Applied Biosystems)

  • Michael Dickson (NetGenics)

  • David Frankel (IONA)

  • Scott Markel (NetGenics)