2016 update of the PRIDE database and its related tools.
2016 update of the PRIDE database and its related tools.
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DOI：
10.1093/nar/gkv1145
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Hermjakob H
中科院分区：
文献类型：
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作者：
Vizcaíno JA;Csordas A;del-Toro N;Dianes JA;Griss J;Lavidas I;Mayer G;Perez-Riverol Y;Reisinger F;Ternent T;Xu QW;Wang R;Hermjakob H
PRoteomics IDEntifications（PRIDE）数据库是世界领先的基于质谱（MS）的蛋白质组学数据库之一。自2014年初以来，PRIDE Archive（http：//www.ebi.ac.uk/pride/archive/）是新的PRIDE存档系统，取代了原来的PRIDE数据库。在这里，我们总结了自2013年数据库问题上的更新手稿以来PRIDE资源和相关工具的发展。PRIDE Archive是对原始PRIDE的完全重新开发，包括新的存储后端、数据提交系统和Web界面等组件。PRIDE Archive支持最广泛使用的PSI（Proteomics Standards Initiative）数据标准格式（mzML和mzIdentML），并实现ProteomeXchange Consortium的数据要求和指导方针。ProteomeXchange在社区内的广泛采用引发了提交数据集数量的前所未有的增长（每月约150个数据集）。我们概述了目前骄傲档案数据内容的一些统计数据。我们还报告了与PRIDE相关的独立工具的状态：PRIDE Inspector，PRIDE Converter 2和ProteomeXchange提交工具。最后，我们将简要介绍正在开发的资源“PRIDE Cluster”和“PRIDE Proteomes”，它们提供了PRIDE Archive中可用的肽和蛋白质鉴定数据的补充视图和质量评分信息。
The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive.