Bittremieux Wout, Kelchtermans Pieter, Valkenborg Dirk, Martens Lennart, Laukens Kris
Department of Mathematics and Computer Science, University of Antwerp , Middelheimlaan 1, B-2020 Antwerp, Belgium.
J Proteome Res. 2014 Jul 3;13(7):3484-7. doi: 10.1021/pr401274z. Epub 2014 Jun 17.
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. First, jqcML provides a complete object model to represent qcML data. Second, 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 .
在过去几年中，人们越来越意识到系统的质量控制是使蛋白质组学发展成为一门成熟分析学科的关键因素。为此，Walzer等人最近提出了一种受控词汇表和文档结构，用于存储和传播基于质谱的蛋白质组学实验的质量控制指标，称为qcML。为了促进这种标准化质量控制程序的采用，我们引入了jqcML，这是一种用于qcML数据格式的Java应用程序编程接口（API）。首先，jqcML提供了一个完整的对象模型来表示qcML数据。其次，jqcML能够以统一的方式读取、写入和处理来自不同来源的qcML数据，包括基于XML的qcML文件格式和关系数据库qcDB。通过Java XML绑定架构（JAXB）实现与基于XML的文件格式的交互，而通过Java持久化API（JPA）获得通用数据库功能。jqcML作为开源软件根据宽松的Apache 2.0许可发布，可从https://bitbucket.org/proteinspector/jqcml下载。
