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 Stoeckert Jr⁵ , Joseph White⁹ , Patricia L Whetzel⁵ , Farrell Wymore⁶ , Helen Parkinson¹ , Ugis Sarkans¹ , Catherine A Ball⁶ and Alvis Brazma¹

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

²Lawrence Berkeley National Laboratory, Berkeley, CA, USA

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

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

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

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

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

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

⁹Dana Farber Cancer Institute, Boston, MA, USA

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

author email corresponding author email

BMC Bioinformatics 2006, 7:489doi: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.