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Healthc Inform Res > Volume 10(3); 2004 > Article
Journal of Korean Society of Medical Informatics 2004;10(3):347-353.
DOI: https://doi.org/10.4258/jksmi.2004.10.3.347    Published online September 30, 2004.
Development of Microarray Gene Expression Database for MicroArray Gene Expression Markup Language
Ji Yeon Park, Se Young Kim, Yu Rang Park, Hwa Jeong Seo, Ju Han Kim
Seoul National University College of Medicine, Biomedical Informatics (SNUBI), Korea.

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.

Key Words: MAGE-OM, MAGE-ML, Microarray, Database, Relational Model


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