The Open Data Exchange Ecosystem in Proteomics: Evolving its Utility

蛋白质组学中的开放数据交换生态系统：进化其效用(ODEEP-EU)项目将在蛋白质组学领域的开放数据交换生态系统中产生关键突破，通过确保基于质谱学的蛋白质组学中的公共数据在遥远的未来能够最大限度地重复使用，这既在蛋白质组学领域，也在整个生命科学领域。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为实现有效的内部再分析和再利用所作的关键努力，三个目标侧重于启动广泛的外部再利用。内部再利用目前关键需要两件事，在前两个目标中解决：(I)为公开可用的数据集提供全面和可靠的元数据；(Ii)提供各种注释非常好和特征仔细的参考数据集，以作为关键的基准、教程和模板材料等。另一方面，生命科学中广泛的外部再利用将由三项协调和直接互补的努力启动，这三项努力将在接下来的三个目标中实现：(3)通过复杂的后处理管道，创建来自蛋白质组学数据的自动信息流，到用于蛋白质序列和上下文信息的UniProt知识库，以及到用于蛋白质结构信息的蛋白质数据库，从而确保生命科学领域的所有研究人员都可以在尽可能广泛的背景下轻松接触和获取这些信息；(4)通过为蛋白质组学数据的再利用提供一个前沿的、以发现为导向的研究展示窗口，重点是阐明蛋白质组范围的PTM发现结果的生物学意义；和(5)大力推动以开放科学为根基的外联和传播努力，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普通公众进行外联。总而言之，在ODEEP-EU，我们可以利用二十年来在蛋白质组学开放科学基础设施建设方面的努力，作为发射台，推动该领域发挥关键作用，成为整个生命科学重要的新知识和见解的绝对无限宝库。

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.