The Open Data Exchange Ecosystem in Proteomics: Evolving its Utility

蛋白质组学开放数据交换生态系统：不断发展其效用（ODEEP-EU）项目将通过确保基于质谱的蛋白质组学的公共数据在未来可以最大限度地重复使用，从而在蛋白质组学领域以及整个生命科学领域实现蛋白质组学开放数据交换生态系统的重大突破。这一总体目标将通过五个目标来实现，其中两个目标侧重于实现有效的内部再分析和重用的关键努力，另外三个目标侧重于启动广泛的外部重用。内部重用现在迫切需要两个关键的东西，在前两个目标中得到解决：(i)为公开可用的数据集提供全面可靠的元数据；（ii）可获得各种非常详细注释和仔细表征的参考数据集，作为关键的基准，教程和模板材料等。另一方面，生命科学领域广泛的外部重复使用将通过三个协调和直接互补的努力来启动，这在以下三个目标中得到了体现：（iii）通过创建一个自动化信息流，从蛋白质组学数据，通过复杂的再处理管道，到UniProt知识库的蛋白质序列和背景信息，到蛋白质数据库的蛋白质结构信息，从而确保所有生命科学领域的研究人员都能在尽可能广泛的背景下轻松地接触和访问这些信息；（iv）通过为蛋白质组学数据重用提供一个前沿的、发现驱动的研究展示，重点是阐明蛋白质组学范围内PTM发现结果的生物学意义；(5)大力推动植根于开放科学的推广和传播工作，包括标准的学术渠道，与工业界的全面和广泛的互动，甚至在全球范围内向公众推广。总之，在ODEEP-EU中，我们可以利用20年来在蛋白质组学开放科学基础设施建设方面的努力，作为启动平台，推动该领域成为重要的新知识和见解的无限宝库的关键角色。

This project Open Data Exchange Ecosystem in Proteomics: Evolving its Utility (ODEEP-EU) will engender a critical breakthrough in the open data exchange ecosystem in proteomics, by ensuring that public data in mass spectrometry-based proteomics can be maximally re-used far into the future, and this both within the field of proteomics, as well as across the life sciences in general. This overall objective will be achieved in five goals, with two goals focused on critical efforts to enable effective internal reanalysis and reuse, and three goals focused on kick-starting widespread external reuse. Internal reuse critically requires two key things right now, tackled in the first two goals: (i) the provision of comprehensive and reliable metadata for publicly available data sets; and (ii) the availability of a variety of very well-annotated and carefully characterised reference data sets to serve as key benchmarking, tutorial, and template materials, amongst others. On the other hand, widespread external re-use across the life sciences will be jump-started by three coordinated and directly complementary efforts, which are captured in the next three goals: (iii) by creating an automated flow of information from proteomics data, over sophisticated reprocessing pipelines, to the UniProt Knowledgebase for protein sequence and context information, and to the Protein Data Bank for protein structural information, thus ensuring that all researchers across the life sciences can easily come across and access this information in the broadest possible context; (iv) by providing a cutting-edge, discovery-driven research showcase for proteomics data re-use, centred on elucidating biological meaning for proteome-wide PTM discovery results; and (v) strongly driven outreach and dissemination efforts that are firmly rooted in open science, and that include standard academic channels, comprehensive and wide-ranging interactions with industry, and even outreach to the general public at a global scale. Taken together, in ODEEP-EU, we can utilise two decades of effort in open science infrastructure establishment in proteomics as the launchpad from which to propel the field into a key role as sheer limitless treasure trove of important novel knowledge and insights for the life sciences at large.