ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.
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DOI：
10.1093/bioinformatics/btv250
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发表时间：
2015-09-01
期刊：
影响因子：
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通讯作者：
Wang R
中科院分区：
文献类型：
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作者：
Perez-Riverol Y;Uszkoreit J;Sanchez A;Ternent T;Del Toro N;Hermjakob H;Vizcaíno JA;Wang R
摘要：MS-DATA核-API是一个免费的开源库，用于开发计算蛋白质组学工具和管道。用Java编写的应用程序编程界面通过提供强大的，可插入的编程接口和常见数据模型来实现快速的工具创建。数据模型基于受控的词汇/本体，并捕获了常见蛋白质组学实验工作流中包含的整个数据类型范围，从光谱到肽/蛋白质识别到定量结果。该库包含三种最常用的蛋白质组学标准标准文件格式的读者：MZML，MZIDENDML和MZTAB。除MZML外，它还支持其他常见的质谱数据格式：DTA，MS2，MGF，PKL，APL，APL（基于文本），MZXML和MZDATA（基于XML）。此外，它可用于读取Pride XML，这是骄傲数据库使用的原始格式，这是世界领先的蛋白质组学资源之一。最后，我们提供了一组算法和工具，其实现说明了使用库的开发应用程序的简单性。
可用性和实现：该软件可在https://github.com/pride-utilities/ms-data-core-api上免费获得。
补充信息：可在线生物信息学上获得补充数据
联系人：juan@ebi.ac.uk
Summary: The ms-data-core-api is a free, open-source library for developing computational proteomics tools and pipelines. The Application Programming Interface, written in Java, enables rapid tool creation by providing a robust, pluggable programming interface and common data model. The data model is based on controlled vocabularies/ontologies and captures the whole range of data types included in common proteomics experimental workflows, going from spectra to peptide/protein identifications to quantitative results. The library contains readers for three of the most used Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab. In addition to mzML, it also supports other common mass spectra data formats: dta, ms2, mgf, pkl, apl (text-based), mzXML and mzData (XML-based). Also, it can be used to read PRIDE XML, the original format used by the PRIDE database, one of the world-leading proteomics resources. Finally, we present a set of algorithms and tools whose implementation illustrates the simplicity of developing applications using the library. Availability and implementation: The software is freely available at https://github.com/PRIDE-Utilities/ms-data-core-api. Supplementary information: Supplementary data are available at Bioinformatics online Contact: juan@ebi.ac.uk