The Swedish Pathogens Portal launch, an important step for pandemic preparedness

Today marks the inauguration of the Swedish Pathogens Portal. Originally introduced as ‘the Swedish COVID-19 Data Portal’, it served as the Swedish node of the European COVID-19 Data Platform. This platform was founded to facilitate the rapid collection and sharing of data essential for fighting the pandemic. Becoming the first national node of the EMBL-EBI Pathogens Portal will allow the Portal, in collaboration with European research infrastructures, to ensure pandemic preparedness.

In July, EMBL-EBI unveiled their latest version of the Pathogens Portal, characterized as a comprehensive “gateway to pathogen data”. This online platform facilitates access for researchers, healthcare professionals, public health agencies, industry representatives, and governmental entities to a vast repository of data related to pathogens. Currently containing data from over 200,000 pathogen species, the Pathogens Portal will be a pivotal instrument for infection biology research and pathogen surveillance, both within Europe and globally. By integrating data from many different sources, the platform ensures that the information is readily accessible. Whilst the portal predominantly features nucleotide sequences, raw genomic data, sample metadata, and relevant scientific literature at present, there are plans to augment its repository with additional public data resources in the future.

“The SciLifeLab Data Centre team is proud that the Portal will be the first national node of the Pathogens Portal. We look forward to continuing to work closely with EMBL-EBI and, together, strive to facilitate sharing of data related to pathogens and facilitate future pandemic preparedness. The Portal will continue to be a central part of the SciLifeLab’s pandemic preparedness efforts,” says Johan Rung, head of SciLifeLab Data Centre.

“Pathogen data sharing is most effective when done collaboratively and across borders,” says Dr Guy Cochrane, Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute. “The Swedish Pathogens Portal is the first national data portal to be connected to the Pathogens Portal at EMBL-EBI, demonstrating the benefits of merging FAIR data resources – meaning Findable, Accessible, Interoperable and Reusable – with national data sharing efforts.”

Since its integration into the SciLifeLab’s Pandemic Laboratory Preparedness (PLP) Program in 2022, the Portal has expanded its scope from solely SARS-CoV-2 to include other pathogens, as well as pandemic preparedness in general. This evolution mirrors the global transition from an exclusive concentration on combating COVID-19 at the pandemic’s peak to a more proactive strategy, aimed at readiness for future pandemics, thereby mitigating their societal impact. Nevertheless, the overall functions of the Portal e.g. guidelines, collected datasets, data-centric articles (data highlights), data dashboards, and community-building features, will remain broadly unchanged compared to earlier iterations.

“The Portal team looks forward to showcasing more data and tools on pathogens besides SARS-CoV-2 and on other pandemic preparedness topics such as antibiotic resistance. Whilst COVID-19 will continue to be an important element of pandemic preparedness efforts, it is now crucial that we begin to make clear that resources developed during the pandemic can be repurposed,” says Liane Hughes, Project lead for the Portal team at SciLifeLab Data Centre.

Moving forward, the Portal remains committed to offering guidelines and support to life science researchers at Swedish universities and institutes. Our aim is to enhance the FAIR (Findable, Accessible, Interoperable, and Reusable) principles and openness of their pandemic preparedness and infectious disease data. The Portal team will continue to work closely with the Editorial Committee, the Data-Driven Life Science (DDLS) community, and the Data Science Nodes, as well as our international partners, such as the BY-COVID consortium, to optimize the Portal’s impact. The research community is encouraged to contact the team behind the Portal for support in data sharing, collaboration opportunities, and feedback.

SciLifeLab Data Centre is a central SciLifeLab unit focused on IT and data management. A dedicated Portal team has developed and maintains the Portal. datacentre@scilifelab.se

Visit the Swedish Pathogens Portal
Visit the EMBL-EBI Pathogens Portal
Meet our Editorial team