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Open Access Highly Accessed Commentary

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Tim F Rayner1*, Philippe Rocca-Serra1, Paul T Spellman2, Helen C Causton3, Anna Farne1, Ele Holloway1, Rafael A Irizarry4, Junmin Liu5, Donald S Maier6, Michael Miller7, Kjell Petersen8, John Quackenbush9, Gavin Sherlock10, Christian J Stoeckert5, Joseph White9, Patricia L Whetzel5, Farrell Wymore6, Helen Parkinson1, Ugis Sarkans1, Catherine A Ball6 and Alvis Brazma1*

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

2 Lawrence Berkeley National Laboratory, Berkeley, CA, USA

3 MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College Hammersmith Hospital Campus, London, UK

4 Department of Biostatistics, John Hopkins School of Public Health, Baltimore, MD, USA

5 Center for Bioinformatics and Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA

6 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA

7 Rosetta Biosoftware, Rosetta Inpharmatics, LLC, Seattle, USA

8 Bergen Center for Computational Science, Computational Biology Unit, University of Bergen, Norway

9 Dana Farber Cancer Institute, Boston, MA, USA

10 Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

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BMC Bioinformatics 2006, 7:489  doi:10.1186/1471-2105-7-489

Published: 6 November 2006

Abstract

Background

Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support.

Results

We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion.

Conclusion

MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.