BeYond-COVID (BY-COVID), a new €12 million Horizon Europe funded project, was recently launched. It will tackle the data challenges that can hinder effectivepandemic response. The core aim of the project is to ensure that data on SARS-CoV-2 andother infectious diseases can be found and used by everyone. ELIXIR Luxembourg and the Bioinformatics Core of the LCSB will participate in one of the work packages of this ambitious European project.
Learning from the COVID-19 crisis
The COVID-19 pandemic continues to affect many lives globally, and it is crucial for us toreflect back on how the scientific community initially responded to the crisis, and whattechnical gaps there were that hindered the ability of scientists to investigate SARS-CoV-2at the early stages of the pandemic. There has been a strong response across the world,with many nations generating and sharing vast amounts of data and locally trackingvariants. Learning from this past experience, and also by monitoring the present daydevelopments of the COVID-19 pandemic we can develop resources, data standards andguidelines that will enable rapid application to novel emerging threats, and specificallyunite and coordinate dispersed datasets from different institutes and countries.
Niklas Blomberg, BY-COVID Coordinator and Director of ELIXIR, spoke of the need to workacross scientific communities in pandemic preparedness: "It is fundamental that we learnand build on the experiences of the COVID-19 pandemic, to ensure that, from a dataperspective, there are no hindrances to rapid access to infectious disease data. The BY-COVID project is a fantastic opportunity to build on the existing infrastructure of the COVID-19 Data Platform, providing opportunities for new knowledge to be generated by integrating data from new disciplines to create a strong foundation for future effective pandemic response"
Incorporating and sharing data efficiently
BY-COVID will build and expand upon the successful COVID-19 Data Platform, a resource initiated in the early stages of the pandemic and led by EMBL-EBI. Since its launch, many countries have established their own national data hubs, which ensures that data produced locally can be instantaneously connected and shared with the main COVID-19 Data Portal. Rather than focus purely on providing technical solutions to the biological data, BY-COVID will work with partners such as the Versatile emerging infectious disease Observatory (VEO) and the Public Health Information Research Infrastructure (PHIRI) to incorporate data from a broader range of disciplines, including public health and social sciences. The BY-COVID project strives to simplify data access and reuse through three main steps:
- Mobilise data
Ensuring raw sequencing data from across the world can be easily submitted to core data hubs (e.g. SARS-CoV-2 Data Hubs, European Nucleotide Archive (ENA), Federated European Genome Archive (FEGA), CESSDA social science archives, and BBMRI biobank directory).
- Connect and expose data
Build the technical capacity to allow linking of sequence data and metadata - expanding beyond scientific and medical data to broader metadata from for example public health and economics. Support integration to the COVID-19 Data Portal.
- Use and analyse data
Provide recommended data management protocols and support analysis of Findable, Accessible, Interoperable and Reusable (FAIR) data on infectious diseases such as the regular VEO reports on mutations and variation in publicly shared SARS-CoV-2 data and the open COVID-19 Galaxy analysis platform.
Several European partners, including ELIXIR-LU and the LCSB
BY-COVID is an exciting interdisciplinary project that unites life science, medical, policy, social science and public health experts from across Europe. Led by ELIXIR, the project has 53 partners from 20 European countries. The BY-COVID project will run for three years and is part of the European Commission's HERA Incubator plan 'Anticipating together the threat of COVID-19 variants'.
Researchers from ELIXIR Luxembourg and the Bioinformatics Core of the LCSB are involved in this project and will participate in work package 5. "BY-COVID emphasises the need to harmonise large, multi-faceted datasets to help dealing with this and future pandemics," explains Dr Marek Ostaszewski, researchers in the Bioinformatics Core. "To this end, it is crucial to have clearly defined use-cases, allowing to focus and guide the efforts of this massive project." The BioCore/ELIXIR-LU team will co-lead one of such use-cases, focusing on the interpretation of viral variants and molecular biology data for a better understanding of the mechanisms behind variant responses.
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