EBI Groups Functional Genomics Documentation ArrayExpress

ArrayExpress Software

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Please before starting to install ArrayExpress software. We are in the middle of redeveloping ArrayExpress infrastructure, and the software available from this page is no longer being developed and will be retired soon.

(You are welcome to use this documentation and scripts on this page, however, we do not take any responsibilities for their use. Please read our license for more details.)

Schema

MAGE-OM is an object model of the microarray gene expression data domain, developed and submitted to Object Management Group (OMG) jointly by MGED and Rosetta to serve as a backbone for standardising gene expression data interchange format and possibly other aspects of gene expression data informatics.

Introduction to MAGE-OM concepts.
MAGE-OM as a set of hyper-linked diagrams.
Another browsable view of MAGE-OM.
MAGE-OM information on MGED.

Implementation

MAGE-OM was used as a source for automatic generation of a relational schema. ArrayExpress runs under Oracle, however no Oracle-specific features have been used and we believe it is easy to port this schema to other database platforms.

It should be emphasised that the mapping from object model to tables is quite simple, where there is a separate table for each class as well as for many-many relations. It is easy to load data into such schema from MAGE-ML (that has also been derived from MAGE-OM), however for purposes of efficient queries some data denormalization is thought to be needed.

For more detailed information, please check out our published paper:
The ArrayExpress gene expression database: a software engineering and implementation perspective. U. Sarkans et al. Bioinformatics, 2005, Vol. 21 No. 8: 1495-1501; doi:10.1093/bioinformatics/bti157 [Abstract] [PDF].

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