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Open Access Software

The XBabelPhish MAGE-ML and XML Translator

Don Maier1*, Farrell Wymore1, Gavin Sherlock2 and Catherine A Ball1

Author Affiliations

1 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA

2 Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA

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BMC Bioinformatics 2008, 9:28  doi:10.1186/1471-2105-9-28

Published: 18 January 2008

Abstract

Background

MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE-ML files are exceptionally large – too large to be easily read by most people, and often too large to be read by most software programs. Second, the MAGE-ML standard permits many ways of representing the same information. As a result, different producers of MAGE-ML create different documents describing the same experiment and its data. Recognizing all the variants is an unwieldy software engineering task, resulting in software packages that can read and process MAGE-ML from some, but not all producers. This Tower of MAGE-ML Babel bars the unencumbered exchange of microarray experiment descriptions couched in MAGE-ML.

Results

We have developed XBabelPhish – an XQuery-based technology for translating one MAGE-ML variant into another. XBabelPhish's use is not restricted to translating MAGE-ML documents. It can transform XML files independent of their DTD, XML schema, or semantic content. Moreover, it is designed to work on very large (> 200 Mb.) files, which are common in the world of MAGE-ML.

Conclusion

XBabelPhish provides a way to inter-translate MAGE-ML variants for improved interchange of microarray experiment information. More generally, it can be used to transform most XML files, including very large ones that exceed the capacity of most XML tools.