Extending the PRIDE database ecosystem: PRIDE-Controlled Access (PRIDE-CA) and the PRIDE-Knowledgebase (PRIDE-KB)

The PRIDE database, established in 2004 at the European Bioinformatics Institute (EMBL-EBI), is the world-leading proteomics data repository.

PRIDE is also the leading partner in the ProteomeXchange Consortium, standardising public proteomics data submission and dissemination worldwide. PRIDE stores ~83% of all ProteomeXchange datasets, with ~5,300 datasets submitted during 2020 alone.

We request support to extend PRIDE, enabling the appropriate handling of clinical sensitive human datasets, through implementing controlled-access (CA) data capabilities.

We will leverage infrastructure implemented for CA DNA/RNA sequencing data in the European Genotype Archive at EMBL-EBI, to create PRIDE-CA.

Additionally, we will adapt the Beacon framework (developed for genetic variation at the DNA level) to support genetic variation data at the protein level, which is increasingly relevant in personalised medicine studies.

We will also develop the PRIDE Knowledge-Base (PRIDE-KB), a complementary resource to PRIDE, to store and disseminate high-quality proteomics data re-analyses, to generate new biological insight.

We will implement proteogenomics data as the first use case supported in PRIDE-KB, reporting protein variants, isoforms and novel coding events for personalised proteomics approaches.

To support this, diverse components will be developed and integrated, including new data archiving infrastructure, web interface, open data analysis pipelines and data inclusion guidelines.