During COVID-19, a network of 12 national-level data portals emerged around the central COVID-19 Data Portal. National data portals serve to provide access and visibility to national-level data services, networks and policy, while the central portal provides access to integrated data services from international repositories and knowledge bases.
Scientists working in a country have rapid and targeted access to resources that are typically organised at the national level, such as clinical trials and national computational facilities, and can then move smoothly across to data services across integrated international data sets. While the data portal network continues to grow for COVID-19, a similar two-level organisation is now being developed for broader ranges of pathogens and diseases.
“One of the most satisfying experiences of our work on COVID-19 was to witness the emergence of a network of national data portals that added local context and services,” said Guy Cochrane, Lead for the European COVID-19 Data Platform at EMBL-EBI. “That this community of data portal providers continues to grow and is extending towards diseases beyond COVID-19 is exciting and will help the world prepare for the next major outbreak.”
In October 2023, the Netherlands launched the Dutch COVID-19 Data Portal and connected it to the existing network of COVID-19 Data Portals.
The Dutch COVID-19 Data Portal supports investigators and health care professionals with tools and services in their search for ways to overcome the pandemic and its health consequences. It incorporates the Dutch National COVID-19 metadata portal, which includes information on COVID-19 related research projects. It also has a dedicated Dutch language servicedesk providing guidance on Ethical, Legal and Societal Impact (ELSI) implications.
“The Dutch COVID-19 & Pandemic Preparedness Data Portal supports investigators and healthcare professionals by providing a hub for datasets, dashboards, events and training, and other resources centred around COVID-19 and pandemic preparedness in the Netherlands,” said Robin Navest, Programme Manager at Lygature. “Furthermore, we provide support for making your data available and are a stepping stone to the European portal, where even more data, tools and services can be found. In the future we aim to shift the focus from COVID-19 towards pandemic preparedness and migrate to a national pathogen portal.”
Extending beyond its National COVID-19 Data Portal, Sweden added the Swedish National Portal in September 2023. During the COVID-19 pandemic, Sweden had been the first country to develop a national COVID-19 Data Portal aiming to accelerate research by supporting FAIR data sharing. This year, the team at SciLifeLab were keen to extend their COVID-19 Portal into a broader preparedness and pathogen data portal based on the same FAIR principles, supporting researchers with submitting and retrieving open data, supporting national collaborations, and creating general guidance and promoting existing resources.
“The SciLifeLab Data Centre team is proud that the Portal will be the first national node of the Pathogens Portal,” said Johan Rung, Head of Data Centre at SciLifeLab. “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.”
The Swedish National Pathogen Data Portal contains pathogen data from multiple research areas such as biochemistry, imaging, drug discovery,as well as public health data. This includes vaccination data, the prevalence of post-COVID-19 conditions, serology data and wastewater surveillance data (going beyond SARS-Cov-2 to include enteric viruses and influenza) from cities across Sweden.
“In 2022, there was a shift in the focus of the global research community towards ensuring better preparedness for future pandemics,” said Liane Hughes, Project Lead at SciLifeLab. “Accordingly, we expanded the scope of our national COVID-19 Portal to include pathogens besides SARS-CoV-2 and pandemic preparedness in general. In order to make this change clear to users, we decided that we needed to rebrand the Portal. Given that the new scope closely reflected that of EMBL-EBI’s Pathogens Portal, and the awareness of that Portal within the global research community, we were thrilled to work with EMBL-EBI to rebrand our national Portal as a national Pathogens Portal.”
Key services and tools provided by the Swedish Pathogen Data and Preparedness Portal include:
An editorial committee advises o the current needs of the Swedish research community.
At a meeting in October 2023, a group of National Data Portals coordinators met to celebrate the launch of the Swedish Pathogen Data Portal, and discuss how to transition other existing COVID-19 Portals into wider scope Pathogen Portals. Under discussion, for example, were presentation of dashboards and scientific publications. The Swedish team made the source code used for the Portal openly available on GitHub, and encourage its reuse for the establishment of further national portals.
“One of the greatest successes of ELIXIR is the long-lasting collaborations between national centres and EMBL-EBI,” said Niklas Blomberg, Director of ELIXIR. “The COVID-19 pandemic really tested this and the COVID-19 Data Portal networks are great examples of how these collaborations rapidly refocused to support research and response to COVID-19. Transforming this response to preparedness via the Pathogens Portal network allow us to sustain this response towards the infectious diseases that will no doubt challenge the world in future.”
The Dutch COVID-19 Data Portal is supported by the Horizon Europe BY-COVID project (Grant Agreement no.101046203) and Health RI.
The Swedish Pathogens Portal is supported by SciLifeLab’s Pandemic Laboratory Preparedness (PLP) Program, the Knut and Alice Wallenberg Foundation (KAW), the Horizon Europe BY-COVID project, and the Swedish Foundation for Strategic Research (SSF).
Coordination of the network is supported by EMBL and the Horizon Europe BY-COVID project.
The European COVID-19 Data Portal and the Pathogens Portal receive support by the following European Union Horizon 2020 and Horizon Europe R&I projects: EOSC-Life (824087), ELIXIR-CONVERGE (871075), BY-COVID(101046203) , VEO (874735) and ReCoDID (825746); and from EMBL-EBI.
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