The Open Data Exchange Ecosystem in Proteomics: Evolving its Utility

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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.