Development of Microarray Gene Expression Database for MicroArray Gene Expression Markup Language.
- Author:
Ji Yeon PARK
1
;
Se Young KIM
;
Yu Rang PARK
;
Hwa Jeong SEO
;
Ju Han KIM
Author Information
1. Seoul National University College of Medicine, Biomedical Informatics (SNUBI), Korea. juhan@snu.ac.kr
- Publication Type:Original Article
- Keywords:
MAGE-OM;
MAGE-ML;
Microarray;
Database;
Relational Model
- MeSH:
Information Storage and Retrieval;
Gene Expression*;
Information Dissemination
- From:Journal of Korean Society of Medical Informatics
2004;10(3):347-353
- CountryRepublic of Korea
- Language:Korean
-
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.
