A proteomics sample metadata representation for multiomics integration and big data analysis.
A proteomics sample metadata representation for multiomics integration and big data analysis.
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用于多组学集成和大数据分析的蛋白质组学样本元数据表示。
DOI：
10.1038/s41467-021-26111-3
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发表时间：
2021-10-06
影响因子：
16.6
通讯作者：
Perez-Riverol Y
中科院分区：
文献类型：
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作者：
Dai C;Füllgrabe A;Pfeuffer J;Solovyeva EM;Deng J;Moreno P;Kamatchinathan S;Kundu DJ;George N;Fexova S;Grüning B;Föll MC;Griss J;Vaudel M;Audain E;Locard-Paulet M;Turewicz M;Eisenacher M;Uszkoreit J;Van Den Bossche T;Schwämmle V;Webel H;Schulze S;Bouyssié D;Jayaram S;Duggineni VK;Samaras P;Wilhelm M;Choi M;Wang M;Kohlbacher O;Brazma A;Papatheodorou I;Bandeira N;Deutsch EW;Vizcaíno JA;Bai M;Sachsenberg T;Levitsky LI;Perez-Riverol Y
公共蛋白质组学数据的数量正在迅速增加，但没有标准化的格式来描述样本元数据及其与数据集文件的关系，以完全支持对它们的理解或重新分析。在这里，我们建议将转录组学数据格式MAGE-TAB开发成蛋白质组学样本元数据的标准表示。我们在一个众包项目中实施MAGE-TAB-Proteomics，以手动管理200多个公共数据集。我们还描述了一些工具和库，用于验证与元数据相关的示例信息并将其提交到PRIDE存储库。我们期望这些发展将提高可重复性，并促进公共蛋白质组学数据集的重新分析和整合。公开可用的蛋白质组学数据集的数量正在迅速增长，但缺乏描述相关元数据的标准化方法。在这里，作者提出了一种格式和软件管道来呈现和验证元数据，并将它们集成到ProteomeXchange存储库中。
The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets. The number of publicly available proteomics datasets is growing rapidly, but a standardized approach for describing the associated metadata is lacking. Here, the authors propose a format and a software pipeline to present and validate metadata, and integrate them into ProteomeXchange repositories.