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MAGE-OM: An object model for the communication of microarray data

Part 4. Bioinformatics

4.7. Structuring and Integrating Data

Short Specialist Review

  1. Catherine A. Ball1,
  2. Paul T. Spellman2,
  3. Michael Miller3

Published Online: 15 APR 2006

DOI: 10.1002/047001153X.g408318

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Ball, C. A., Spellman, P. T. and Miller, M. 2006. MAGE-OM: An object model for the communication of microarray data. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.7.

Author Information

  1. 1

    Stanford University School of Medicine, Department of Biochemistry, Stanford, CA, US

  2. 2

    Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, US

  3. 3

    Rosetta Inpharmatics, Seattle, WA, US

Publication History

  1. Published Online: 15 APR 2006

Abstract

Meaningful exchange of many high-throughput biological data is difficult without sufficient information depth and without well-accepted data formats. Microarray data can be exchanged with the Microarray Gene Expression Markup Language (MAGE-ML), which is based on a conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (Microarray Gene Expression Object Model). MAGE was (and continues to be) developed in a collaborative and cooperative manner by many members of the grass-roots Microarray Gene Expression Data Society (MGED). The MAGE- OM was developed with the express intent to provide enough depth and breadth to fully capture data required to meet the standards for the minimum information annotating a microarray experiment (MIAME). MAGE developers and adopters have contributed to a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems. Future plans include developing a second version of MAGE-OM that will reduce ambiguities, completely integrate the MGED Ontology, fully capture higher level analysis steps and will be broad enough to contribute to a greater object model for a superset of large-scale biomedical technologies, called Functional Genomics (FuGE).

Keywords:

  • microarray;
  • object model;
  • data exchange;
  • markup language;
  • software