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EMBL-EBI launches COVID-19 Data Portal
EMBL-EBI launches COVID-19 Data Portal
20 April, Cambridge – EMBL’s European Bioinformatics Institute (EMBL-EBI) and partners today launched the COVID-19 Data Portal, which enables the sharing and analysis of data related to the new coronavirus, SARS-CoV-2. The initiative aims to facilitate international collaboration to accelerate scientific discovery, monitor the pandemic and help develop treatments and a vaccine for the new coronavirus.
An international effort
Since the start of the COVID-19 pandemic, thousands of researchers across the globe have been working tirelessly to study the new coronavirus. They have generated an enormous amount of information, but until now there has been no central repository for this information.
The COVID-19 Data Portal addresses this need, creating a shared space where data about the new coronavirus can be stored, shared and analysed using tools developed by EMBL-EBI and the wider scientific community.
“No single institute or country can tackle this pandemic,” explains Rolf Apweiler, Director of EMBL-EBI. “ We have to work together and share data in an open, sustainable and smart way. As the home for the world’s biological data, EMBL-EBI is well placed to develop a data-sharing infrastructure for COVID-19, but we need the help of collaborators in Europe and around the world to grow this new portal.”
A multitude of data types
Currently, the COVID-19 Data Portal includes datasets from the following EMBL-EBI data resources:
- European Nucleotide Archive (ENA)
- Protein Data Bank in Europe (PDBe)
- Electron Microscopy Data Bank (EMDB)
- Expression Atlas
- Europe PMC
These resources cover a wide range of data types including genomic, protein and microscopy data, as well as scientific literature.
In the coming weeks, the portal will also include genomic data from the outbreak and a dedicated Cohort Browser for searching clinical and epidemiological data.
“Users can upload their SARS-CoV-2 data and get access to data from other sources around the world,” says Guy Cochrane, Team Leader for Data Coordination and Archiving at EMBL-EBI. “We’re working hard to make the portal intuitive and easy to use. The portal also features data analysis and visualisation tools to help interpret the data.”
The COVID-19 Data Portal will evolve to contain a wide selection of data types, including the ones in the table below.
|Data type||What does it allow us to do?|
|Genomic data (viral and human)||
Understand the biology of the virus
Monitor the spread of infection
|Protein structure and function data||
Understand how the virus interacts with other moleculesIdentify potential treatments and vaccine
Understand the biology of the virusUnderstand how the virus interacts with other molecules
|Proteomics data||Understand the biology of the virus|
|Metabolomics data||Identify potential treatments and vaccine|
|Chemical compound and drug target data||Identify potential treatments and vaccine|
|Gene expression data||Understand the biology of the virus|
Understand how human body reacts to the infectionObserve how the virus is changing
|Epidemiological data||Monitor the spread of the infection|
|Scientific literature||See what experiments have already taken place and what they found|
Ramping up efforts
In the coming weeks and months, additional datasets and tools from other European projects will be added to the COVID-19 Data Portal. With the help of ELIXIR, the intergovernmental organisation that brings together life science data and resources from across Europe, and with the help of other collaborators, the COVID-19 Data Portal will continue to grow.
"Science, public health and healthcare have to work together if we want to minimise the impact of the COVID-19 pandemic,” says Marion Koopmans, Head of the Viroscience Department of Erasmus Medical Centre in Rotterdam, and a collaborator in the COVID-19 Data Portal project. “We are hoping that this initiative will enable researchers, clinicians and public health workers to safely and efficiently share their data in order to come up with answers to the most pressing questions about COVID-19.”
Part of a wider European response
The COVID-19 Data Portal is the entry point to the wider European COVID-19 Data Platform initiative, which involves the creation of multiple SARS-CoV-2 Data Hubs. These hubs are currently being built and, once ready, will organise the flow of sequence data from the outbreak and provide comprehensive open data sharing for the European and global research communities accessible through the Data Portal.
“Launching the European COVID-19 Data Platform is an important concrete measure for stronger cooperation in fighting the coronavirus,” says European Commissioner Mariya Gabriel. “Building on our dedicated support for open science and open access over the years, now is the time to step up our efforts and stand united with our researchers. Through our joint efforts, we will better understand, diagnose and eventually overpower the pandemic.”
Both the European COVID-19 Data Portal and the SARS-CoV-2 Data Hubs will use already established EMBL-EBI data infrastructures, including the Pathogen Portal and the European Nucleotide Archive (ENA). The latter is part of the COMPARE Data Hubs, which provide pathogen-focused data sharing and analysis tools, and will be connected to the European Open Science Cloud (EOSC).
The European COVID-19 Data Platform is one of the ten projects included in the first iteration of the ERAvsCORONA Action Plan launched by the European Commission.
“We need Open Science now more than ever before,” says Kostas Glinos, Head of the Open Science Unit of the European Commission. "Sharing data and knowledge at such an unprecedented speed will help us win the battle against the pandemic. We are very happy to work with EMBL-EBI and the other partners in this common effort.”
Explore the COVID-19 Data Portal to see the available data and how you can submit data.
- Erasmus Medical Centre (Netherlands)
- Technical University of Denmark
- Eötvös Loránd University (Hungary)
- National Institute for Public Health and the Environment (Netherlands)
- Universitaetsklinikum Heidelberg (Germany)