Research
Design and implementation of microarray gene expression markup language (MAGE-ML)
1 Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720-3206, USA
2 Rosetta Biosoftware, 113th Ave NE, Kirkland, WA 98034, USA
3 Open Informatics, Arizona St SE, Albuquerque, NM 87108, USA
4 Bioscience Research - Agilent Technologies, Deer Creek Rd, Palo Alto, CA 94304, USA
5 European Bioinformatics Institute, EMBL Hinxton Outstation, Cambridge CB10 1SD, UK
6 Affymetrix, Inc., Vallejo St, Emeryville, CA 94608, USA
7 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
8 Molecular Mining Corporation, Rideau St, Kingston, ON K7K 2Z8, Canada
9 Imaging Research Inc., Glenridge Ave, St. Catharines, ON L2S 3A1, Canada
10 Iobion Informatics LLC, North Torrey Pines Road, La Jolla, CA 92037, USA
11 LION bioscience Inc., Executive Drive, San Diego, CA 92121, USA
12 Center for Bioinformatics, University of Pennsylvania, Guardian Drive, Philadelphia, PA 19104, USA
13 The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA
14 Computational Biology, Institute for Systems Biology, North 34th St, Seattle, WA 98103-8904, USA
15 CHRF, Burnet Ave, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
Genome Biology 2002, 3:research0046-research0046.9 doi:10.1186/gb-2002-3-9-research0046
Published: 23 August 2002Abstract
Background
Meaningful exchange of microarray data is currently difficult because it is rare that published data provide sufficient information depth or are even in the same format from one publication to another. Only when data can be easily exchanged will the entire biological community be able to derive the full benefit from such microarray studies.
Results
To this end we have developed three key ingredients towards standardizing the storage and exchange of microarray data. First, we have created a minimal information for the annotation of a microarray experiment (MIAME)-compliant conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE-OM (microarray gene expression object model). Second, we have translated MAGE-OM into an XML-based data format, MAGE-ML, to facilitate the exchange of data. Third, some of us are now using MAGE (or its progenitors) in data production settings. Finally, we have developed a freely available software tool kit (MAGE-STK) that eases the integration of MAGE-ML into end users' systems.
Conclusions
MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
