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

Kenny Helsens UGent, Mi-Youn Brusniak, Eric Deutsch, Robert L Moritz and Lennart Martens UGent (2011) JOURNAL OF PROTEOME RESEARCH. 10(11). p.5260-5263
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PROTEOMICS, ASSAYS, PLASMA-PROTEINS, MASS-SPECTROMETRY, standards, selection reaction monitoring, mass spectrometry, bioinformatics, proteomics, VALIDATION, DATABASE
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
10
issue
11
pages
5260 - 5263
Web of Science type
Article
Web of Science id
000296414700034
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
5.113 (2011)
JCR rank
10/72 (2011)
JCR quartile
1 (2011)
ISSN
1535-3893
DOI
10.1021/pr200664h
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1966508
handle
http://hdl.handle.net/1854/LU-1966508
date created
2011-12-13 16:29:37
date last changed
2016-12-19 15:42:18
@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},
}

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.