{"id":1344,"date":"2025-05-08T16:20:38","date_gmt":"2025-05-08T14:20:38","guid":{"rendered":"https:\/\/c29ugbqilr.preview.infomaniak.website\/?post_type=portfolio&p=1344"},"modified":"2025-05-20T13:14:41","modified_gmt":"2025-05-20T11:14:41","slug":"open-spsp-a-swiss-wide-platform-to-open-viral-and-bacterial-sequences-and-clinical-epidemiological-data-to-researchers-world-wide-while-preserving-patient-privacy","status":"publish","type":"portfolio","link":"https:\/\/spsp.ch\/fr\/portfolio\/open-spsp-a-swiss-wide-platform-to-open-viral-and-bacterial-sequences-and-clinical-epidemiological-data-to-researchers-world-wide-while-preserving-patient-privacy\/","title":{"rendered":"Open-SPSP: A Swiss-wide platform to open viral and bacterial sequences and clinical\/epidemiological data to researchers world-wide, while preserving patient privacy"},"content":{"rendered":"

Project description<\/h4>\n

To respond efficiently to outbreaks and pandemics such as Covid-19, open and rapid access of
\nresearchers to sequencing data produced at clinical centers is essential, as exemplified by the UK
\nmutation uncovered in December. Currently, national SARS-CoV-2 data hubs organise the flow of viral
\nsequences coming from laboratories all over Europe to a central European portal via the European
\nNucleotide Archive (ENA). These open resources allow reusing and analyzing the data to researchers
\nworld-wide. Unfortunately, Switzerland does not have such a national data hub that facilitates Open
\nsharing of data, likely explaining that less than 600 sequences were published on the Covid-19 portal
\nso far. In order to enable Swiss clinical laboratories to submit in a few clicks, in real-time, their
\nsequences to ENA, we propose to extend the existing “Swiss Pathogen Surveillance Platform”, a
\nsecure online platform for pathogen sequencing data and their associated sensitive
\nclinical\/epidemiological metadata.<\/p>\n

This will not only allow incorporating Swiss data in research projects
\nworldwide, it will also bring Switzerland within the network of national data hubs for future strategic
\ndevelopments. With this project, we will in particular (i) facilitate the data upload to SPSP to foster near
\nreal-time data submissions with optimized e-accessibility. (ii) Develop a module to automatically
\npublish to ENA genomic data and their associated, non-sensitive, metadata. Reciprocally, we will also
\nimport into SPSP the genomes available on NCBI\/ENA with their limited metadata to enable Swiss
\nresearchers to address research questions using the rich metadata on Swiss strains alongside strains
\ncollected elsewhere. (iii) Setup a secure computation server with analysis tools, for users with ethical
\napprovals to address research questions on SPSP sensitive data that could not be published on ENA.
\nAltogether, our project will make SPSP data Open when possible, and FAIR where patient-privacy
\nissues apply.<\/p>\n

Results<\/h4>\n

As of May 2025, SPSP is still one of the top SARS-CoV-2 open data submitters to the European Covid-19 Data Portal.<\/p>\n

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