Design and implementation of microarray gene expression markup language (MAGE-ML).
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.
Spellman
Paul T
PT
Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720-3206, USA. spellman@fruitfly.org
Miller
Michael
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Stewart
Jason
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Troup
Charles
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Sarkans
Ugis
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Chervitz
Steve
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Bernhart
Derek
D
Sherlock
Gavin
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Ball
Catherine
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Lepage
Marc
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Swiatek
Marcin
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Marks
W L
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Goncalves
Jason
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Markel
Scott
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Iordan
Daniel
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Shojatalab
Mohammadreza
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Pizarro
Angel
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White
Joe
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Hubley
Robert
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Deutsch
Eric
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Senger
Martin
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Aronow
Bruce J
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Robinson
Alan
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Bassett
Doug
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Stoeckert
Christian J
CJ
Brazma
Alvis
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D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods