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jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions

(2011) JOURNAL OF PROTEOME RESEARCH. 10(11). p.5260-5263
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com. TraML files can also be converted online at http://iomics.ugent.be/jtraml.
Keywords
PROTEOMICS, ASSAYS, PLASMA-PROTEINS, MASS-SPECTROMETRY, standards, selection reaction monitoring, mass spectrometry, bioinformatics, proteomics, VALIDATION, DATABASE

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Citation

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Chicago
Helsens, Kenny, Mi-Youn Brusniak, Eric Deutsch, Robert L Moritz, and Lennart Martens. 2011. “jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions.” Journal of Proteome Research 10 (11): 5260–5263.
APA
Helsens, K., Brusniak, M.-Y., Deutsch, E., Moritz, R. L., & Martens, L. (2011). jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. JOURNAL OF PROTEOME RESEARCH, 10(11), 5260–5263.
Vancouver
1.
Helsens K, Brusniak M-Y, Deutsch E, Moritz RL, Martens L. jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions. JOURNAL OF PROTEOME RESEARCH. 2011;10(11):5260–3.
MLA
Helsens, Kenny, Mi-Youn Brusniak, Eric Deutsch, et al. “jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions.” JOURNAL OF PROTEOME RESEARCH 10.11 (2011): 5260–5263. Print.
@article{1966508,
  abstract     = {We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com. TraML files can also be converted online at http://iomics.ugent.be/jtraml.},
  author       = {Helsens, Kenny and Brusniak, Mi-Youn and Deutsch, Eric and Moritz, Robert L and Martens, Lennart},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {PROTEOMICS,ASSAYS,PLASMA-PROTEINS,MASS-SPECTROMETRY,standards,selection reaction monitoring,mass spectrometry,bioinformatics,proteomics,VALIDATION,DATABASE},
  language     = {eng},
  number       = {11},
  pages        = {5260--5263},
  title        = {jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions},
  url          = {http://dx.doi.org/10.1021/pr200664h},
  volume       = {10},
  year         = {2011},
}

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