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Open Access Highly Accessed Software

A software framework for microarray and gene expression object model (MAGE-OM) array design annotation

Matloob Qureshi and Alasdair Ivens*

Author Affiliations

Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK

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BMC Genomics 2008, 9:133  doi:10.1186/1471-2164-9-133

Published: 20 March 2008

Abstract

Background

The MIAME and MAGE-OM standards defined by the MGED society provide a specification and implementation of a software infrastructure to facilitate the submission and sharing of data from microarray studies via public repositories. However, although the MAGE object model is flexible enough to support different annotation strategies, the annotation of array descriptions can be complex.

Results

We have developed a graphical Java-based application (Adamant) to assist with submission of Microarray designs to public repositories. Output of the application is fully compliant with the standards prescribed by the various public data repositories.

Conclusion

Adamant will allow researchers to annotate and submit their own array designs to public repositories without requiring programming expertise, knowledge of the MAGE-OM or XML. The application has been used to submit a number of ArrayDesigns to the Array Express database.