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 Stoeckert Jr¹² and Alvis Brazma⁵

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

⁴Bioscience Research - 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

author email corresponding author email

Genome Biology 2002, 3:research0046.1-0046.9doi:10.1186/gb-2002-3-9-research0046


Published:	23 August 2002

Subject areas: Bioinformatics, Methods, Genome studies

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.