Visualisation module

1

MIAMExpress New Components Web Service,
ADF-MAGEML Converter,Visualization tool, Batch
Upload
Catherine Leroy, Pierre Marguerite, Bhuwan
Tiwari, Niran Abeygunawardena, Sergio Contrino,
Anna Farne, Ele Holloway, Gaurab Mukherjee,
Helen Parkinson, Tim Rayner, Philippe
Rocca-Serra, Susanna-Assunta Sansone, Ugis
Sarkans, Alvis Brazma and Mohammadreza Shojatalab
Microarray Informatics Team, EMBL - European
Bioinformatics Institute, U.K.

• Abstract
• MIAMExpress is a microarray data annotation and
  submission tool, which allows entry of MIAME
  compliant information and exports MAGE-ML files
  1. The tool is widely used as the submission
  tool to ArrayExpress database, and data from over
  4000 hybridisations have been entered this way.
  Here we present three new modules for MIAMExpress
  tool visualisation module, batch-upload module,
  and ADF to MAGE-ML file converter module. These
  will be implemented as a part of the next
  MIAMExpress release.
• A 'Visualization Module' will allow users to
  navigate their submission in a very intuitive
  manner. The tool, relying on Graphviz, converts
  results from SQL queries into graphs. Samples,
  Extracts, Labeled Extracts and Hybridizations are
  shown as boxes, directed arrows show the
  relationships between elements. Those are
  hyperlinked back to the relevant MIAMExpress web
  forms allowing seamless access for
  altering/completing submission.
• A 'Batch-upload Module' will allow to bridge the
  usability gap that currently exists between
  small-medium sized experiments and large scale
  projects submissions. Web service technology will
  be integrated in a java client allowing a
  spreadsheet like display of the various layers of
  information necessary to describe a microarray
  experiment in MIAMExpress. Providing connexion to
  MIAMExpress database will ensure that updated
  controlled vocabulary can be used throughout the
  submission process.
• An 'ADF-MAGE-ML converter Standalone Module' will
  allow creation of Array Design Files (ADF) and
  conversion to MAGE-ML documents and vice versa,
  in batch mode or one at a time. The specification
  has been extended to provide support for other
  DNA microarray applications ranging from gene
  expression to comparative genomic hybridization
  and chromatin binding site identification.
•  

Architecture
Dealing with Affymetrix submissions Merger
module
Any Other Java or .NET Client On Any OS or
Architecture
MIAMExpress Batch Upload Application
MIAMExpress Web Interface User
To deal with submissions on Affymetrix arrays
more efficiently, a tool has been developed
called MyGD using Affymetrix GDAC Exporter
library to prduce MAGE-ML file in a batch fashion
from each submitted hybridization and this
MAGE-ML file contains BioAssay,BioAssayData and
Protocol packages. On the other hand MIAMExpress
produce a MAGE-ML file which describe annotation
of samples, Biomaterials, experiment design,
experimental factors and factor values,
Bibliographic references. To create a single
MAGE-ML file in which all these packages come
together a Merging module has been developed
which consolidates all MAGE-ML files into a
single MAGE-ML file.
Curators at EBI
MAGEML/ADF Producer/Consumer
MyGD Application
MIAMExpress Web Service
Main CGI module
MAGE-ML
MAGExpress (MAGE-ML creator module)
Visualisation module
GUI modules
MAGExpress (MAGE-ML creator module)
ADFlt-gtMAGE-ML Converter Standalone application
One MAGE-ML file per Hybridization
Merger Module
MAGE-ML
MAGE-STK
MAGE-STK
MyGD
MIAMExpress API
MIAMExpress API
Affymetrix GDAC Exporter
Database access Layer
Database access Layer
DBI
DBI
MIAMExpress MySQL Database
File System
MIAMExpress MySQL Database
File System

Visualization ADF MAGE-ML Converter Batch
upload MyGD
Controlled Vocabulary
adc
All the node are clickable and permit to display
the corresponding submission form.
Node corresponding to the sample of the Sample
Annotation page below
adr
adh
Array Design File (ADF) three files
Sample upload using Batch Upload Application
Experiment visualization screen
Hybridization upload using Batch Upload
Application
MIAMExpress Sample Annotation Screen
MAGE-ML File

• Next Release
• All 3 new modules will be released with
  MIAMExpress version 2.0 and will be implemented
  in all community specific versions of the tool
  Tox-MIAMExpress and At-MIAMExpress.
• Alongside with the mentioned new components there
  are some other new features which are going to be
  part of the next release
• Curator (perl programs developed by curators and
  useful for curation activities)
• Auto-Update Agent to be used in local
  installations to get the bug-fixes more
  efficiently
• Ability to upload compressed data files to
  overcome the bandwidth problem in uploading large
  data files
• Access to public protocols in ArrayExpress as
  well as public Array designs in ArrayExpress,
  both in EBIs MIAMExpress and local
  installations.
• Support for export of FactorValues
• Full compliancy with Best Practice
• (http//www.ebi.ac.uk/miamexpress/)

Acknowledgements The ArrayExpress database has
been partly supported by EMBL budget, European
Commission (TEMBLOR-DESPRAD), Biostandards,
AstraZeneca, ILSI Health and Environmental
Sciences Institute (HESI), Compendium of
Arabidopsis Gene Expression (CAGE), and Incyte
Genomics. References 1. ArrayExpress - a public
repository for microarray gene expression data at
the EBI. (2003) Brazma, A. et al. Nucleic Acids
Res. 31(1)68-71.

EMBL European Bioinformatics Institute Wellcome
Trust Genome Campus EMBL Outstation Hinxton,
Cambridge CB10 1SD UNITED KINGDOM
http//www.ebi.ac.uk/miamexpress Shoja_at_ebi.ac.uk