The XBabelPhish MAGE-ML and XML Translator

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.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.Researchers using DNA microarrays in their studies are widely encouraged, and sometimes compelled by journals or funding agencies, to increase the usefulness of their individual research efforts by making their experimental information easily accessible to the community at large. Conversely, many researchers would like to gain easy access to microarray data from other experimenters' work. The need to exchange and aggregate large-scale biomedical data motivates requirements for universal and easy-to-use tools and file formats to do this. This, in turn, has engendered efforts to describe microarray experiments in a standard way.The need for a standard format led to the development of the Microarray Gene Expression Markup Language (MAGE-ML) [1], a standardized Extensible Markup Language (XML) format for describing microarray experiments and their result data. Unfortunately, some characteristics of actual documents have limited MAGE-ML's usefulness as a standard. Specifically:MAGE-ML documents can be so large that most native XML viewing and transformation tools are unable to open them. Also, even if MAGE-ML documents were typically of a more modest size that allowed viewing and editing tools to digest them, most working experimental biologists find the XML format challenging to "parse" visually and are unfamiliar with those XML tools that try to ameliora