Design and implementation of microarray gene expression markup language (MAGE-ML)
Genome Biology 2002, 3(9):research0046.1–0046.9

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 White³, Robert Hubley¹⁴, Eric Deutsch¹⁴, Martin Senger⁵, Bruce J Aronow¹⁵, Alan Robinson⁵, Doug Bassett², Christian J Stoeckert Jr¹² and Alvis Brazma⁵

Addresses:
¹Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, CA 94720-3206, USA.
²Rosetta Biosoftware, 113th Ave NE, Kirkland, WA 98034, USA.
³Open Informatics, Arizona St SE, Albuquerque, NM 87108, USA.
⁴BioscienceResearch - Agilent Technologies, Deer Creek Rd, Palo Alto, CA 94304, USA.
⁵European Bioinformatics Institute, EMBL Hinxton Outstation, Cambridge CB10 1SD, UK.
⁶Affymetrix, Inc., Vallejo St, Emeryville, CA 94608, USA.
⁷Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.
⁸Molecular Mining Corporation, Rideau St, Kingston, ON K7K 2Z8, Canada.
⁹Imaging Research Inc., Glenridge Ave, St. Catharines, ON L2S 3A1, Canada.
¹⁰Iobion Informatics LLC, North Torrey Pines Road, La Jolla, CA 92037, USA.
¹¹LION bioscience Inc., Executive Drive, San Diego, CA 92121, USA.
¹²Center for Bioinformatics, University of Pennsylvania, Guardian Drive, Philadelphia, PA 19104, USA.
¹³The Institute for Genomic Research, Medical Center Drive, Rockville, MD 20850, USA.
¹⁴Computational Biology, Institute for Systems Biology, North 34th St, Seattle, WA 98103-8904, USA.
^15CHRF, Burnet Ave, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.

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.