The XBabelPhish MAGE-ML and XML Translator
<p>Abstract</p> <p>Background</p> <p>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 exceptiona...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-01-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/9/28 |
| _version_ | 1819175300718657536 |
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| author | Sherlock Gavin Wymore Farrell Maier Don Ball Catherine A |
| author_facet | Sherlock Gavin Wymore Farrell Maier Don Ball Catherine A |
| author_sort | Sherlock Gavin |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-22T20:52:41Z |
| format | Article |
| id | doaj.art-d1b791b66fdf4252b47e089afd0c0e87 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-22T20:52:41Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-d1b791b66fdf4252b47e089afd0c0e872022-12-21T18:13:03ZengBMCBMC Bioinformatics1471-21052008-01-01912810.1186/1471-2105-9-28The XBabelPhish MAGE-ML and XML TranslatorSherlock GavinWymore FarrellMaier DonBall Catherine A<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/9/28 |
| spellingShingle | Sherlock Gavin Wymore Farrell Maier Don Ball Catherine A The XBabelPhish MAGE-ML and XML Translator BMC Bioinformatics |
| title | The XBabelPhish MAGE-ML and XML Translator |
| title_full | The XBabelPhish MAGE-ML and XML Translator |
| title_fullStr | The XBabelPhish MAGE-ML and XML Translator |
| title_full_unstemmed | The XBabelPhish MAGE-ML and XML Translator |
| title_short | The XBabelPhish MAGE-ML and XML Translator |
| title_sort | xbabelphish mage ml and xml translator |
| url | http://www.biomedcentral.com/1471-2105/9/28 |
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