Periodic Reporting for period 2 - BY-COVID (Beyond COVID)
Période du rapport: 2023-04-01 au 2024-09-30
As seen during the COVID-19 pandemic, and other infectious disease outbreaks, researchers, healthcare professionals and citizens need to store, share, access, analyse, link and process research and clinical data and data analysis workflows across disciplines and national borders in a coordinated response.
Boosting FAIR and open data sharing in support for European preparedness for COVID-19 and other infectious diseases, BY-COVID worked to:
enable researchers, healthcare professionals and citizens fighting the spread of infectious diseases to store, document, share, access, analyse, link and process research and clinical data across disciplines and national borders;
federate research and clinical data (human and viral) through national and international centres, to enable pan-European and global sharing and hence research advances for better preparedness;
develop the necessary digital tools and data analytics, including for the identification and tracking of variants of concern, in support of public health action;
improve linkages of FAIR data (and associated metadata) on pathogens, on their diseases and on their socio-economic consequences, considering a range of research fields, such as omics, clinical, and epidemiological research, social sciences & humanities, to take a holistic approach to preparedness and response.
The BY-COVID project also worked to ensure that these efforts usefully contributed to the European Open Science Cloud (EOSC) Partnership and the European Health Data Space (EHDS).
Boosting FAIR and open data sharing in support for European preparedness for COVID-19 and other infectious diseases, BY-COVID worked to:
enable researchers, healthcare professionals and citizens fighting the spread of infectious diseases to store, document, share, access, analyse, link and process research and clinical data across disciplines and national borders;
federate research and clinical data (human and viral) through national and international centres, to enable pan-European and global sharing and hence research advances for better preparedness;
develop the necessary digital tools and data analytics, including for the identification and tracking of variants of concern, in support of public health action;
improve linkages of FAIR data (and associated metadata) on pathogens, on their diseases and on their socio-economic consequences, considering a range of research fields, such as omics, clinical, and epidemiological research, social sciences & humanities, to take a holistic approach to preparedness and response.
The BY-COVID project also worked to ensure that these efforts usefully contributed to the European Open Science Cloud (EOSC) Partnership and the European Health Data Space (EHDS).
The course of the COVID-19 pandemic was shaped from the outset by Open Science; the early public deposition of the original sequences in January 2020 drove the development of the tests and vaccines and formed the baseline against which the public health impact of novel variants was observed. It has been estimated that over 14 million deaths were prevented in 2021 alone.
Starting in October 2021, the BY-COVID project has developed the European contribution to the international framework for sharing and re-using data - initially focused on COVID-19 and the European COVID-19 Data Platform, but subsequently investing effort in future pandemic preparedness and putting effort into the development of a general purpose Pathogens Portal based on the same principles and making use of the same approaches and underlying indexing mechanisms. The Pathogens Portal is complemented by a Pathogen Data Hub capability, which researchers can use to prepare their data for pre-publication analysis and eventual public deposition; and a growing network of national pathogens portals which can respond to local needs and guidance on the pathogens of concern in different geographical regions.
The practice of data mobilisation, ensuring that data sets are FAIR and Open wherever possible, has made use of the network of resources built and recommended by the BY-COVID partners - services such as FAIRsharing, WorkflowHub, Galaxy, the Clinical Research Data Sharing Repository, the BioImage Archive and the European Nucleotide Archive. These resources are not specific to pathogens, but with rich metadata can be used to provide access to pathogen datasets while also benefiting from the support and development of these resources across domains and through infrastructure programmes such as the European Open Science Cloud and future European Health Data Space. The consortium partners themselves have built a core of pathogens expertise and will continue to support the development of collections and metadata to keep these systems relevant to future outbreak response.
The use and re-use of these services and data sets across domains and stakeholders is a complex topic and we have built the Infectious Disease Toolkit to help scientists find the services and databases they need to contribute to the activities of the global pathogens community. Together with multilingual citizen science material produced during the project, and as part of a developing international network and policy framework for pathogen data sharing, the examples studied during BY-COVID (for example in causal modelling, wastewater surveillance, and clinical trial data re-use) and the recommendations for data FAIRification and mobilisation will support future pandemic research, preparedness and response.
Starting in October 2021, the BY-COVID project has developed the European contribution to the international framework for sharing and re-using data - initially focused on COVID-19 and the European COVID-19 Data Platform, but subsequently investing effort in future pandemic preparedness and putting effort into the development of a general purpose Pathogens Portal based on the same principles and making use of the same approaches and underlying indexing mechanisms. The Pathogens Portal is complemented by a Pathogen Data Hub capability, which researchers can use to prepare their data for pre-publication analysis and eventual public deposition; and a growing network of national pathogens portals which can respond to local needs and guidance on the pathogens of concern in different geographical regions.
The practice of data mobilisation, ensuring that data sets are FAIR and Open wherever possible, has made use of the network of resources built and recommended by the BY-COVID partners - services such as FAIRsharing, WorkflowHub, Galaxy, the Clinical Research Data Sharing Repository, the BioImage Archive and the European Nucleotide Archive. These resources are not specific to pathogens, but with rich metadata can be used to provide access to pathogen datasets while also benefiting from the support and development of these resources across domains and through infrastructure programmes such as the European Open Science Cloud and future European Health Data Space. The consortium partners themselves have built a core of pathogens expertise and will continue to support the development of collections and metadata to keep these systems relevant to future outbreak response.
The use and re-use of these services and data sets across domains and stakeholders is a complex topic and we have built the Infectious Disease Toolkit to help scientists find the services and databases they need to contribute to the activities of the global pathogens community. Together with multilingual citizen science material produced during the project, and as part of a developing international network and policy framework for pathogen data sharing, the examples studied during BY-COVID (for example in causal modelling, wastewater surveillance, and clinical trial data re-use) and the recommendations for data FAIRification and mobilisation will support future pandemic research, preparedness and response.
The BY-COVID project’s goal of accelerating Open Data for European preparedness for infectious diseases served as a driver for increased collaboration, mobilisation of FAIR datasets to maximise re-use and impact, and cross-domain approaches to data to answer complex public health policy questions.
The maturity of the high-profile COVID-19 Portal was significantly enhanced, with many more datasets and whole new data types added to its indexes. The Pathogens Portal, a service for all pathogens researchers, will serve multiple roles - accumulating knowledge through periods of research and acting as a key reference through periods of emergency outbreak response.
A network of pathogen data professionals was developed, with the Infectious Disease Toolkit knowledge base as their tool to save and share experiences and best practices. The development of a network of national and local portals and hubs was enabled and has led to the foundation of an international Pathogen Data Network. This network of practice was deployed in the ISIDORe project, accelerating Research infrastructure services for rapid research responses to COVID-19 and other infectious disease epidemics, and led to the recommendation of ‘Umbrella Data Management Plans’ to Integrate FAIR Data in families of related projects.
The project engaged with the EOSC Partnership, demonstrating the impact of EOSC-developed services such as WorkflowHub, and provide driving use cases (such as answering causal research questions using data visiting, and building wastewater surveillance monitoring solutions) which will inform the design of the EHDS. The development of Clinical Research Data Sharing Repository contributed to the development of a Europe-wide practice of data sharing.
The maturity of the high-profile COVID-19 Portal was significantly enhanced, with many more datasets and whole new data types added to its indexes. The Pathogens Portal, a service for all pathogens researchers, will serve multiple roles - accumulating knowledge through periods of research and acting as a key reference through periods of emergency outbreak response.
A network of pathogen data professionals was developed, with the Infectious Disease Toolkit knowledge base as their tool to save and share experiences and best practices. The development of a network of national and local portals and hubs was enabled and has led to the foundation of an international Pathogen Data Network. This network of practice was deployed in the ISIDORe project, accelerating Research infrastructure services for rapid research responses to COVID-19 and other infectious disease epidemics, and led to the recommendation of ‘Umbrella Data Management Plans’ to Integrate FAIR Data in families of related projects.
The project engaged with the EOSC Partnership, demonstrating the impact of EOSC-developed services such as WorkflowHub, and provide driving use cases (such as answering causal research questions using data visiting, and building wastewater surveillance monitoring solutions) which will inform the design of the EHDS. The development of Clinical Research Data Sharing Repository contributed to the development of a Europe-wide practice of data sharing.