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Visualisation module

Internet. New. New. New. New. MIAMExpress New Components : Web Service, ADF-MAGEML Converter,Visualization tool, Batch Upload.

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Visualisation module

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  1. Internet New New New New 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 Main CGI module MIAMExpress Web Service MAGE-ML MAGExpress (MAGE-ML creator module) Visualisation module GUI modules MAGExpress (MAGE-ML creator module) ADF<->MAGE-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 EBI’s 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@ebi.ac.uk

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