Title
jqcML : an open-source Java API for mass spectrometry quality control data in the qcML format jqcML : an open-source Java API for mass spectrometry quality control data in the qcML format
Author
Faculty/Department
Faculty of Sciences. Biology
Faculty of Sciences. Mathematics and Computer Science
Publication type
article
Publication
Subject
Chemistry
Biology
Computer. Automation
Source (journal)
Journal of proteome research
Volume/pages
13(2014) :7 , p. 3484-3487
ISSN
1535-3893
ISI
000338693400032
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
Abstract
The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality control metrics for mass spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. Firstly, jqcML provides a complete object model to represent qcML data. Secondly, jqcML provides the ability to read, write and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml.
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