J Korean Soc Med Inform.  2004 Sep;10(3):347-353.

Development of Microarray Gene Expression Database for MicroArray Gene Expression Markup Language

• Park JY
• Kim SY
• Park YR
• Seo HJ
• Kim JH

Abstract

OBJECTIVE
Gene expression microarrays become a widely used tool in biomedicine. With growing needs of microarray data sharing, there are efforts for the development of microarray standards. MAGE-OM(Microarray Gene Expression Object Model) is a data exchange model and MAGE-ML is an XML-based data exchange format. Most database, however, do not have a suitable structure for MAGE-ML storage and maximum use of the data. Therefore, we have created relational database implementing MAGE-OM for the storage of MAGE-ML with importing and exporting capabilities.
METHODS
A relational schema is derived from MAGE-OM with simple object-relational mapping strategy to reduce complexity of MAGE-OM. Data transfer between database and MAGE-ML document is performed via MAGE-OM using the MAGE Software Toolkit(MAGEstk).
RESULTS
Our database accepts microarray data as MAGE-ML files through web-based interface, classifying into two types of submission, array or experiment. MAGE-ML import-export function is flexible to accommodate changing data model by separating model definition and implementation layers.
CONCLUSION
Standard-based implementation of gene expression database enhances the collection and the structured storage of large-scale gene expression data from heterogeneous data sources.

Keyword

MAGE-OM; MAGE-ML; Microarray; Database; Relational Model

MeSH Terms

Information Storage and Retrieval
Gene Expression*
Information Dissemination