Arrayexpress and mage jamboree ii
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ArrayExpress and MAGE Jamboree II. Ugis Sarkans, EBI. Outline. what is ArrayExpress overall architecture status and future MAGE Jamboree II. ArrayExpress. EBI’s public gene expression data repository

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Arrayexpress and mage jamboree ii

ArrayExpress and MAGE Jamboree II

Ugis Sarkans, EBI


Outline

Outline

  • what is ArrayExpress

  • overall architecture

  • status and future

  • MAGE Jamboree II


Arrayexpress

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


Class diagram

Classdiagram


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

  • www.ebi.ac.uk/arrayexpress


Arrayexpress features

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


Arrayexpress component architecture

ArrayExpress component architecture

User

Web server

API

application server

(Java servlets)

MIAMEexpress

submission/

curation tool

database

ArrayExpress

data warehouse

(gene-centred

queries)

central database

(experiment-centred

queries)

curation

MAGE-ML

image server


Arrayexpress architecture

ArrayExpress architecture

MAGE-OM

ArrayExpress

(Oracle)

MAGE-ML

(DTD)

data

loader

Tomcat

object/

relational

mapping

Castor

MAGE-ML (doc)

MAGE-ML (doc)

MAGE-ML (doc)

Java servlets

Velocity

template

engine

MIAMEexpress

Web page

template

submission/

curation tool

database

Web page

template

Browser


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 - under development:

    • queries:

      • by experiment

      • by array

      • by sample

    • browsing


Queries

Queries


Arrayexpress and mage jamboree ii

Sample description


Near future developments

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)


Future developments

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)


Mage jamboree ii

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


Programming apis

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


Programming apis cont

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


Magestk components

MAGEstk components

MAGE-RS

(database)

MAGE-ML

MAGE API

(Perl, Java, C++)

MAGE browsing/

annotation tools


Arrayexpress and mage jamboree ii

Acknowledgements

  • 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


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