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jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, VizcaĆ­no JA - Proteomics (2014)

Bottom Line: mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches.The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files.In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science and Technology, Hubei University of Education, Wuhan, China.

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Simplified UML diagram of the jmzTab API. The classes are structured in three different layers: the Core Model Layer (highlighted in gray), the Enhancement Utilities Layer (dark-gray), and the Standalone Application Layer (white). See main text for more details. The diagram does not include all the classes and methods.
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fig01: Simplified UML diagram of the jmzTab API. The classes are structured in three different layers: the Core Model Layer (highlighted in gray), the Enhancement Utilities Layer (dark-gray), and the Standalone Application Layer (white). See main text for more details. The diagram does not include all the classes and methods.

Mentions: jmzTab is structured in a three-layer architecture: (i) the Core Model Layer, a lightweight independent implementation for maintaining the integrity between the different sections in the file; (ii) the Enhancement Utilities Layer, which provides parsing, validation, and conversion functionality; and (iii) the Standalone Application Layer, which constitutes the centralized graphical user interface (GUI) and command line entry point for the conversion and validation functionality. The main classes of the Core Model are displayed as an UML (Unified Modified Language) diagram in Fig.1. Detailed documentation about how to use the API can be found at https://code.google.com/p/mztab/wiki/jmzTab2 and at http://mztab.googlecode.com/svn/jmztab/trunk/docs/index.html.


jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, VizcaĆ­no JA - Proteomics (2014)

Simplified UML diagram of the jmzTab API. The classes are structured in three different layers: the Core Model Layer (highlighted in gray), the Enhancement Utilities Layer (dark-gray), and the Standalone Application Layer (white). See main text for more details. The diagram does not include all the classes and methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230411&req=5

fig01: Simplified UML diagram of the jmzTab API. The classes are structured in three different layers: the Core Model Layer (highlighted in gray), the Enhancement Utilities Layer (dark-gray), and the Standalone Application Layer (white). See main text for more details. The diagram does not include all the classes and methods.
Mentions: jmzTab is structured in a three-layer architecture: (i) the Core Model Layer, a lightweight independent implementation for maintaining the integrity between the different sections in the file; (ii) the Enhancement Utilities Layer, which provides parsing, validation, and conversion functionality; and (iii) the Standalone Application Layer, which constitutes the centralized graphical user interface (GUI) and command line entry point for the conversion and validation functionality. The main classes of the Core Model are displayed as an UML (Unified Modified Language) diagram in Fig.1. Detailed documentation about how to use the API can be found at https://code.google.com/p/mztab/wiki/jmzTab2 and at http://mztab.googlecode.com/svn/jmztab/trunk/docs/index.html.

Bottom Line: mzTab is the most recent standard format developed by the Proteomics Standards Initiative. mzTab is a flexible tab-delimited file that can capture identification and quantification results coming from MS-based proteomics and metabolomics approaches.The second key feature of the jmzTab model is that it provides a flexible framework to maintain the logical integrity between the metadata and the table-based sections in the mzTab files.In this article, as two example implementations, we also describe two stand-alone tools that can be used to validate mzTab files and to convert PRIDE XML files to mzTab.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Computer Science and Technology, Hubei University of Education, Wuhan, China.

Show MeSH