The XBabelPhish MAGE-ML and XML translator.

BMC Bioinformatics
Don MaierCatherine A Ball

Abstract

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. 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-tra...Continue Reading

References

Sep 13, 2002·Genome Biology·Paul T SpellmanAlvis Brazma
Dec 20, 2007·Nucleic Acids Research·UNKNOWN Rice Annotation ProjectManuel Echeverria

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Citations

Sep 8, 2012·Reproduction, Fertility, and Development·Tiziana PacchiariniElsa Cabrita
May 2, 2008·Omics : a Journal of Integrative Biology·Susanna-Assunta SansoneUNKNOWN Members of the RSBI Working Group
Jun 18, 2009·BMC Bioinformatics·Yu QianRyan R Brinkman
Mar 31, 2012·PloS One·Yanjun QiWilliam Stafford Noble

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Software Mentioned

Galax
XBabelPhish DB XML
ShreX
XSLT
Berkeley DB
SQL
Microarray Gene Expression Markup Language ( MAGE - ML )
eXist
trang
changeLocationQuery

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