The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards
The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards
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DOI：
10.1074/mcp.m111.008334
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发表时间：
2011-10-01
影响因子：
7
通讯作者：
Albar, Juan P.
中科院分区：
文献类型：
--
作者：
Alberto Medina-Aunon, J.;Martinez-Bartolome, Salvador;Albar, Juan P.
HUPO-PSI(蛋白质组学标准倡议)标准数据格式和MIAPE(蛋白质组学实验最小信息)指南的开发应该会改善科学界内的蛋白质组学数据共享。蛋白质组学期刊鼓励使用这些标准和指南，以提高实验报告的质量，并简化手稿的评估和发表。然而，显然缺乏专门设计的生物信息学工具来创建和编辑标准文件格式和报告，或将它们嵌入蛋白质组学工作流中。在这篇文章中，我们描述了一个新的基于网络的软件套件(ProteoRed MIAPE网络工具包)，它扮演着与蛋白质组数据标准相关的几个互补角色。首先，它可以验证报告是否满足相应MIAPE模块的最低信息要求，突出显示不一致或缺失的信息。其次，该工具包可以将几个基于XML的数据标准直接转换为存储在ProteoRed MIAPE存储库中的人类可读的MIAPE报告。最后，它还可以执行相反的操作，允许用户将MIAPE报告导出为XML文件，用于计算处理、数据共享或公共数据库提交。因此，该工具包是第一个能够自动将PSI的MIAPE模块与相应的XML数据交换标准链接起来的应用程序，从而实现双向转换。该工具包可在http://www.proteored.org/MIAPE/.上免费获得分子与细胞蛋白质组学10：10.1074/mcp.M111.008334，1-8,2011年。
The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/. Molecular & Cellular Proteomics 10: 10.1074/mcp.M111.008334, 1-8, 2011.