Research article summary (published 16 Jan 2008):

The XBabelPhish MAGE-ML and XML translator.

Full 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.

Author information

Author/s: Maier, Don (D); Wymore, Farrell (F); Sherlock, Gavin (G); Ball, Catherine A (CA);

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA. dMaier(-atsign-)genome.stanford.edu

Grants: P41 HG003619 (Agency:NHGRI NIH HHS)

Journal and publication information

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal: BMC bioinformatics (BMC Bioinformatics), published in England. (Language: eng)

Reference: 2008-; vol 9 (issue ) : pp 28

Dates: Created 2008/02/07; Completed 2008/03/27; Revised 2008/11/20;

PMID: 18205924, status: MEDLINE (last retrieved date: 2/18/2009)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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MeSH headings (categories)

This article was linked to the MeSH Headings (categories) shown below.

Animals Database Management Systems Gene Expression Profiling - methods Humans Hypermedia

Information Storage and Retrieval - methods Oligonucleotide Array Sequence Analysis - methods Systems Integration User-Computer Interface Work Simplification

Note: Bold headings indicate primary MeSH headings or qualifiers.

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