The PRIDE database: A proteomics data hub in the life sciences

Established in 2004 at EMBL-EBI, PRIDE is the world-leading proteomics data repository and, since 2011, is leading the ProteomeXchange Consortium, standardising public proteomics data submission and dissemination worldwide. The success of PRIDE and ProteomeXchange, has largely driven the proteomics community to widely embracing open data policies. To continue serving and shaping this increasingly prominent field, we primarily request support for the further development of PRIDE as a repository, to enable an efficient handling of proteomics ‘big data’ such as the increasingly large datasets generated from clinical studies. A key component is the development of a submission Application Programming Interface that can be integrated in third-party software. Second, PRIDE will become a Hub for proteomics data, by establishing robust data dissemination pipelines to key resources (UniProt, Ensembl/Ensembl Genomes, Expression Atlas), enabling proteomics data reuse by all biological researchers. We will build novel, open quality control pipelines to ensure that only high-quality data is propagated. Third, also to facilitate data reuse, we will develop and make available open, reproducible proteomics data analysis pipelines tailored for multi-omics approaches used e.g. in personalised medicine. These pipelines will be connected to PRIDE, bringing cutting-edge analysis tools closer to the data, as datasets become larger.