The use of the COVID-19 Data Portal enables European and global research communities to upload, access, and analyse relevant reference data and specialised datasets.
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Initiatives involved
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Disciplinary fields
Challenge
At the beginning of the COVID-19 pandemic, three significant challenges were recognised: The need to rapidly mobilise open biomolecular data, mobilise new SARS-CoV-2 data, and connect to clinical and epidemiological data. Providing open access to the COVID-19 Data Portal has facilitated data sharing and analysis worldwide and accelerated coronavirus research, serving as the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
Solution
The COVID-19 Data Portal was developed to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. The portal includes relevant datasets submitted to EMBL-EBI as well as other major centres for biomedical data. The COVID-19 Data Portal is the primary entry point into the functions of a wider project, the European COVID-19 Data Platform.
Specific examples of how the service has provided solutions include:
- Nextstrain uses open data from the COVID-19 Data Portal (raw data, consensus sequences and variant calls) to provide an open-source toolkit enabling SARS-CoV-2 bioinformatics and visualisation.
- Open Targets "Target Prioritisation Tool" made available via the COVID-19 Data Portal. This tool enables users to retrieve data from such resources as Ensembl, UniProt and ChEMBL and provide analysis and curation to derive prioritisation lists of compounds with potential activities against genomics targets known or suspected to be of relevance to COVID-19.
- Galaxy CRG provides a collection of Galaxy workflows for the detection and interpretation of sequence variants in SARS-CoV-2 on their Global platform for SARS-Cov-2 analysis. Galaxy uses the raw data obtained from the COVID-19 Portal/ENA to analyse and generate consensus sequences/variant calls and feed it into their CRG Viral Beacon variant browser, providing analyses and visualizations to the global community.
Impact
The data made available through the COVID-19 Data Portal have been used by various global resources to create their toolkits and workflows; similarly, the Portal uses input from global resources. The establishment of the COVID-19 Data Portal helped to achieve the objectives of the EOSC-Life project to create an open, digital and collaborative space for biological and medical research. By serving as the primary entry point, it also supported the goals of a wider project, the European COVID-19 Data Platform.
For more information visit the European Life Science Research Infrastructures website.
