The Pathogens Portal, maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and partners, was launched in July 2023. The Pathogens Portal is a resource for e.g. researchers, clinicians, and policymakers. Its aim is to facilitate access to the latest and most comprehensive datasets on pathogens. The COVID-19 pandemic put a spotlight on the importance of data sharing and for focused access to relevant datasets. Therefore, the Pathogens Portal was developed as a centralised platform for data sharing and accessing data on key pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. Bringing together data from a number of sources, and linking data contributes to a better understand Pathogen ́s Biology. Funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: RECODID, VEO, EOSC-Life, CONVERGE and BY-COVID. Moving forward, national nodes of the Pathogens Portal will be added, the Swedish Pathogens Portal is the first to launch in Sept 2023.
European COVID-19 Data Platform
The Swedish Pathogens Portal was originally launched as the ‘Swedish COVID-19 Data Portal’ and it was a national node of the European COVID-19 Data Platform. The European COVID-19 Data Platform is operated by the European Bioinformatics Institute (a part of the European Molecular Biology Laboratory (EMBL-EBI)), together with the European Commission, and other research partners, such as ELIXIR. An overview of other national nodes can be found here.
The European COVID-19 Data Platform aims to facilitate data sharing and analysis in order to accelerate coronavirus research. It enables researchers to upload, access and analyse reference data and specialist datasets related to COVID-19. It is synchronised with COVID-19-related data and scientific literature held in EMBL-EBI's data resources, including ENA, UniProt, PDBe, EMDB, Expression Atlas and Europe PMC. The data continues to grow in diversity and volume, but include sequences, structures, expression data, compound screens, biochemistries and scientific publications.
The Swedish Pathogens Portal is one of the partners in the BY-COVID consortium. BY-COVID is a Horizon project funded by the European Comission and brings together 53 partners from 19 countries. Stakeholders include individuals and organisation from multiple areas, including the biomedical field, hospitals, public health, social sciences and humanities.
The BeYond-COVID (BY-COVID) project aims to make COVID-19 data accessible to anyone that can use it, including medical staff in hospitals, researchers in labs, and government officials. The project will provide a framework for making data from other infectious diseases open and accessible to everyone. The project will integrate established national and European infrastructures with ELIXIR, BBMRI, ECRIN, PHIRI and CESSDA. It will build on existing efforts, such as the COVID-19 Data Platform and the Versatile Emerging infectious disease Observatory project (VEO), in order to maximise efficiency. It will also develop synergies with the European Health Data Space.
Members of the Portal team are involved in the development of the Infectious Disease Toolkit, a major deliverable of the BY-COVID project.
NBIS and ELIXIR Sweden
NBIS (National Bioinformatics Infrastructure Sweden) is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities, and the Knut and Alice Wallenberg Foundation. It provides state-of-the-art bioinformatics to the life science research community in Sweden. NBIS is also the Swedish contact point to the European infrastructure for biological information, ELIXIR Europe.
GA4GH is an international, non-profit organisation focused on advancing the responsible and effective sharing of genomic and health-related data. GA4GH aims to establish harmonised frameworks and standards in order to promote data interoperability and collaboration in genomics research and healthcare. At the same time, the alliance focuses on fully protecting the human rights of people who share their data. GA4GH brings together experts from various sectors, including academia, industry, and government, to address the ethical, legal, and technical challenges associated with genomic data sharing.
The Infectious Disease Community, a vital component of the GA4GH, plays a crucial role in bridging the realms of pathogen and host genomics. This community brings together international groups dedicated to standardising the use of genomic data for improved diagnosis and treatment of infectious diseases. International groups within the community collaborate to identify opportunities for sharing datasets, workflows, and processes, enabling them to address complex and previously insurmountable questions. Through these collective activities, the Infectious Disease Community facilitates the advancement of genomic research, ultimately leading to improved diagnostic and treatment approaches for infectious diseases.