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Design and implementation of microarray gene expression markup language (MAGE-ML)

Paul T Spellman1*, Michael Miller2, Jason Stewart3, Charles Troup4, Ugis Sarkans5, Steve Chervitz6, Derek Bernhart6, Gavin Sherlock7, Catherine Ball7, Marc Lepage8, Marcin Swiatek9, WL Marks10, Jason Goncalves10, Scott Markel11, Daniel Iordan10, Mohammadreza Shojatalab5, Angel Pizarro12, Joe White13, Robert Hubley14, Eric Deutsch14, Martin Senger15, Bruce J Aronow15, Alan Robinson5, Doug Bassett2, Christian J Stoeckert12 and Alvis Brazma5

Author affiliations

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

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Citation and License

Genome Biology 2002, 3:research0046-research0046.9  doi:10.1186/gb-2002-3-9-research0046

Published: 23 August 2002

Abstract

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.