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The XBabelPhish MAGE-ML and XML translator.

Maier D, Wymore F, Sherlock G, Ball CA - BMC Bioinformatics (2008)

Bottom Line: As a result, different producers of MAGE-ML create different documents describing the same experiment and its data.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.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH
XBabelPhish run output. The running commentary that XBabelPhish gives of its progress executing the translation of Figure 1 on the file snipped into Figure 3. The -verbose option has been used to provide more detail.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 5: XBabelPhish run output. The running commentary that XBabelPhish gives of its progress executing the translation of Figure 1 on the file snipped into Figure 3. The -verbose option has been used to provide more detail.

Mentions: Figure 5 is the run output of XBabelPhish performing the example translation. By default, XBabelPhish gives a modest running commentary on its progress. The -verbose option used in Figure 5, provides more details.


The XBabelPhish MAGE-ML and XML translator.

Maier D, Wymore F, Sherlock G, Ball CA - BMC Bioinformatics (2008)

XBabelPhish run output. The running commentary that XBabelPhish gives of its progress executing the translation of Figure 1 on the file snipped into Figure 3. The -verbose option has been used to provide more detail.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2233607&req=5

Figure 5: XBabelPhish run output. The running commentary that XBabelPhish gives of its progress executing the translation of Figure 1 on the file snipped into Figure 3. The -verbose option has been used to provide more detail.
Mentions: Figure 5 is the run output of XBabelPhish performing the example translation. By default, XBabelPhish gives a modest running commentary on its progress. The -verbose option used in Figure 5, provides more details.

Bottom Line: As a result, different producers of MAGE-ML create different documents describing the same experiment and its data.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.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH