MicroArray Gene Expression Markup Language 바이오 데이터 표준을 구현한 유전체 발현정보 데이터베이스 구축
Development of Microarray Gene Expression Database for MicroArray Gene Expression Markup Language
2
조회
0
다운로드
0
인용
0
참고문헌
초록
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.
참고문헌 (12)
- "Genomic Medicine^Bio-Medical Informatics", 9((2):), pp.79~89 (2003)
- "Gene expression databases and data mining", pp.36~44 (2003)
- "Microarray databases: standards and ontologies", pp.469~73 (2002)
- "MGED - Microarray Gene Expression Data Society"
- "The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database(SMD).", 4((1):) (2003)
- "RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.", pp.452~459 (2004)
- "Design and implementation of microarray gene expression markup language", RESEARCH00460046.9.(9), pp.1~0046.9. (2002)
- "Gene Expression SpecificationVersion 1.0, OMG 2003.", pp.~1 (2003)
- "Database Design for Microarray Data Exchange Model MAGE-OM", 9((3):), pp.227~234 (2003), l
- "A Survey on Efficient XML Storage Methods over Various Repository", 19((1):), pp.1~14 (2003)
- "ArrayExpress - a public repository for microarray gene expression data at the EBI", 31((1):), pp.68~71 (2003)
- "An object model and database for functional genomics", 20((10):), pp.1583~1590 (2004)