arrayexpress and mage jamboree ii
Download
Skip this Video
Download Presentation
ArrayExpress and MAGE Jamboree II

Loading in 2 Seconds...

play fullscreen
1 / 18

ArrayExpress and MAGE Jamboree II - PowerPoint PPT Presentation


  • 101 Views
  • Uploaded on

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

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'ArrayExpress and MAGE Jamboree II' - carlo


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
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
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
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

slide18
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
ad