Design and implementation of microarray gene expression markup language (MAGE-ML) |
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Authors: | Spellman Paul T Miller Michael Stewart Jason Troup Charles Sarkans Ugis Chervitz Steve Bernhart Derek Sherlock Gavin Ball Catherine Lepage Marc Swiatek Marcin Marks W L Goncalves Jason Markel Scott Iordan Daniel Shojatalab Mohammadreza Pizarro Angel White Joe Hubley Robert Deutsch Eric Senger Martin Aronow Bruce J Robinson Alan Bassett Doug Stoeckert Christian J Brazma Alvis |
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Institution: | Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720-3206, USA. spellman@fruitfly.org |
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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. |
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