TRANSCRIPTOME 2002: From Functional Genomics to Systems
ArrayExpress - A Public Database for Microarray Data
Slides: PowerPoint or Web version
Helen Parkinson, European Bioinformatics Institute, Cambridge, UNITED KINGDOM
The handling and analysis of the huge amounts of microarray data is becoming the major bottleneck in microarray analysis. Storing and annotation of microarray data is a non trivial problem due to the size, complexity and of the datasets. The raw image data presents particular storage problems and the annotation and integration of sample and array annotation with existing genomic data is essential for maximum interpretability of the data.
The EBI as is a member MGED (Microarray Gene Expression Database Group) which is involved in an international effort to standardise the way that microarray data are represented with guidelines for which information should be supplied with the microarray data (www.mged.org). This standard is called MIAME (Minimum Information About a Microarray Experiment (Brazma et al., 2001).
The EBI is establishing a database - ArrayExpress, to store MIAME compliant data (Brazma et al., 2000). An object model -MAGE-OM, for ArrayExpress has been developed and submitted to the OMG (Object Management Group) for acceptance as an specification for expression data. An XML data exchange format, MAGE-ML has been generated from the model. Datasubmissions to ArrayExpress can be made in MAGE-ML format or via the submission tool MIAMExpress, a web based tool under development at the EBI (http://www.ebi.ac.uk/miamexpress/) for submission of MIAME compliant data.
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