The Swedish COVID-19 Data Portal one year on - focus on openly sharing data and code
Published: 2021-06-03
The COVID-19 pandemic has constituted a global public health crisis over the last year and a half. This crisis has driven the need for accelerated research into the unknown SARS-COV-2 virus and the new COVID-19 disease. In response, the global research community swiftly refocused their efforts to meet the demand for the rapid development of novel therapies and vaccines. The unprecedented speed of this response was made possible in part by the open sharing of data and code, which increased the opportunities for data reuse and the fostering of collaborations. The Swedish COVID-19 Data Portal is part of the effort to maximise the sharing of data and code.
In the spring of 2020, the European Commission took the initiative to develop a European data sharing platform for COVID-19 research efforts, operated by the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI). One year ago today, on June 3rd 2020, the Swedish COVID-19 Data Portal was launched as the first national node of this platform. The Portal has been developed and is operated by the SciLifeLab Data Centre and partners on assignment from the Swedish Research Council.
The Swedish COVID-19 Data Portal provides guidance, tools, and services for finding and sharing research data made available by Swedish and international researchers. Since its launch, the Swedish COVID-19 Data Portal has had >22,000 visitors and >100,000 pageviews and the portal team has provided support for a wide range of research projects.
“As the team behind the Portal, we are all happy about the very positive response to our work. The COVID-19 Data Portal is currently visited mostly by the research community, but we also get visitors working in healthcare and the press, as well as visitors from the general public,” says Katarina Öjefors Stark, a research coordinator working in the Portal team.
The Portal website comprises a number of services launched over the last year. For example, anyone looking for data and/or code can make use of discipline-specific, manually curated lists of openly shared data and/or code that have been made available by researchers affiliated with a Swedish research institute. Those wishing to make use of biomaterials and data accumulated in biobanks across Sweden will find the the Swedish COVID-19 Sample Collection Database useful. This database, developed in collaboration with Biobank Sweden, allows researchers to look for biomaterial collections matching their criteria (it is possible to perform searches based on materials, diagnosis, sample collection types). The database contains biobanks and sample collections from both healthcare and academia. To date, it contains information about 29 sample collections from 16 different biobanks. Another service within the Portal is a manually curated database of publications on COVID-19 and SARS-CoV-2 that lists all published articles and preprints involving at least one author affiliated with a Swedish research institute. To date, the publication database contains information on over 1300 publications.
In addition to guidance available on the Portal website, practical data management support is also offered by the SciLifeLab Data Centre Data Management team and partners. Almost 200 projects have been in contact with the support team over the last year.
The Swedish COVID-19 Data Portal also works to increase the visibility of publications/projects by producing news items called Data Highlights. In particular, the Data Highlights promote work in which data and/or code is shared openly, so that it can potentially be reused by other researchers to make further discoveries, and also work in which new discoveries were made by reusing existing data and/or code.
The Portal also provides a place for various community-driven projects to publish their results or reach researchers in Sweden. Among the general public and policy-makers, the section of the Portal displaying recent SARS-CoV-2 testing results has been especially popular. This section contains regularly updated results from antibody testing carried out at the SciLifeLab Autoimmunity and Serology profiling facility as well as from the analyses of wastewater across Sweden. The Portal also has sections dedicated to partner projects, currently including CRUSH Covid and COVID Symptom Study Sweden (but we are always on the lookout for new partners).
“All code developed for the Portal has been shared on GitHub under an open source licence. As the underlying code for the Portal is freely available on GitHub, parts of it have been reused by a number of teams in other countries in order to rapidly develop their own national portals. This means that the Portal itself functions as a demonstration of the value of openly sharing code,” says Arnold Kochari, one of the web developers in the Portal team.
Finally, the Portal team has multiple plans for the future. For example, work is ongoing to develop new sections and visualisations that should be made available later in 2021. The COVID-19 pandemic is now in a new phase in Sweden, where the vaccination coverage is increasing and vaccine research is coming into focus. The Portal is planning to launch corresponding sections devoted to vaccine research in the near future. Recently, the COVID-19 Data & Code Reuse Competition was launched by the Portal. In this competition, both researchers and the general public are invited to prepare small projects that make use of publicly available data and/or code to combat the COVID-19 and future pandemics.
Johan Rung, Head of SciLifeLab Data Centre and leader for the Portal team says: “Moving forward, the COVID-19 Data Portal will build on the features already developed and made available during the last year. In addition, just as the societal response to the pandemic is currently in the process of moving towards vaccines and future pandemic preparedness, the Portal will develop new features to meet these new needs. We are thankful for researchers that choose to share their data and code, as this allows for new analyses, which not only leads to new results and new knowledge, but also increases reproducibility. Our aim is to further improve our support to the important community efforts involved in responding to this pandemic.”
The team behind the Swedish COVID-19 Data Portal always welcomes collaboration suggestions, questions about publishing and finding data, data management in general, and any feedback regarding the Portal itself. Please do not hesitate to get in touch with us using our contact form or by sending us an email to datacentre@scilifelab.se.
Below you can watch a short video describing the Portal and demonstrating some of the sections.