Periodic Reporting for period 3 - EOSC-Life (Providing an open collaborative space for digital biology in Europe)
Période du rapport: 2022-03-01 au 2023-08-31
Research data in the life sciences is rapidly increasing in size and complexity and many datasets are beyond what can be handled, shared and analysed by a single organisation. In addition, access to large, high-quality datasets sparks data-driven research and is essential for Europe’s competitiveness in areas such as artificial intelligence and personalised medicine. The purpose of EOSC-Life was to ensure that data - and the tools and workflows used to produce and analyse the data - is made findable, accessible, interoperable and reusable so that data produced in public European life-science research can be utilised to the fullest extent, both within and beyond the original project.
EOSC-Life - the life science cluster in EOSC - brought together the 13 ESFRI Life Science Research Infrastructures (LS RIs) in Europe to create an open, collaborative digital space for life science in the European Open Science Cloud (EOSC). Through the project LS RI data is published as FAIR Data Resources, linked to reusable tools and workflows that can be accessed within standardised computing services in national life-science clouds. EOSC-Life also connected users across Europe to a single login authentication and resource authorisation system (LS Login), and developed the data policies needed to preserve and deepen the trust given by research participants and patients volunteering their data and samples.
The success of EOSC-Life means that European scientists will have access to advanced data services, technology platforms, samples and support services throughout the European Research Area (ERA), and the resulting data will be openly accessible for reuse through EOSC. The LS Login system is now used as a basis for the secure sharing of human genomic data through the European Genomics Data Infrastructure programme.
EOSC-Life - the life science cluster in EOSC - brought together the 13 ESFRI Life Science Research Infrastructures (LS RIs) in Europe to create an open, collaborative digital space for life science in the European Open Science Cloud (EOSC). Through the project LS RI data is published as FAIR Data Resources, linked to reusable tools and workflows that can be accessed within standardised computing services in national life-science clouds. EOSC-Life also connected users across Europe to a single login authentication and resource authorisation system (LS Login), and developed the data policies needed to preserve and deepen the trust given by research participants and patients volunteering their data and samples.
The success of EOSC-Life means that European scientists will have access to advanced data services, technology platforms, samples and support services throughout the European Research Area (ERA), and the resulting data will be openly accessible for reuse through EOSC. The LS Login system is now used as a basis for the secure sharing of human genomic data through the European Genomics Data Infrastructure programme.
The EOSC-Life project resulted in the publication of nearly 200 peer-reviewed and non-peer-reviewed (preprints, reports) publications, plus 47 deliverables. In addition, EOSC-Life was able to provide important services to researchers of COVID-19 in response to EC/ERA requests. As such, EOSC-Life has been instrumental in delivering the European COVID-19 Data Portal. The work in the project delivery was organised around four goals:
1. Publish FAIR life science data resources in EOSC:
Here the LS RI data catalogue (https://fairsharing.org/3513) was published and training and hackathons build capacity for cloud deployment of life sciences data. The data publishing and LS RI catalogue have formed the basis for future pandemic preparedness through the European COVID-19 Data Portal and the BY-COVID project, as well as supporting work towards the cancer mission in EOSC4Cancer. RO-Crate was adopted as a model for FAIR data Objects. Formal standards for Provenance Information Management (ISO 23494-1) and the Common Provenance Model (ISO 23494-2) provide a foundation for reproducibility and reusability of data within EOSC. EOSC-Life also supported the COVID-19 Data Portal (https://www.covid19dataportal.org).
2. Provide policies, guidelines and a toolkit for secure and ethical data reuse:
The EOSC-Life sensitive data toolbox helps data providers make their sensitive data available for secondary use. This includes data access procedures, requirements for hosting/distributing and access control mechanisms for sensitive data (including Access and Benefit Sharing via Nagoya Protocol).
3. Populated an ecosystem of innovative life science tools in EOSC:
EOSC-Life established a EOSC-compatible roadmap to support and guide the development of cloud-based workflows by RIs and released WorkflowHub.eu a public registry for computational workflows. The EOSC-Life tools ecosystem has been adopted within other domains, e.g environmental sciences and astronomy. The LS Login system is fully operational (https://lifescience-ri.eu/ls-login.html) and provides common authentication and authorization services for secure federated access in EOSC.
4. Enable data-driven research in Europe by connecting life scientists to EOSC via Open Calls for participation:
EOSC-Life organised Open Calls for data and user projects were successful with 11 external partnership projects selected from 91 applications. All user projects are now concluded with reports publicly available on the EOSC-Life website. Data, workflows and other digital research artefacts are deposited as FAIR digital objects in suitable repositories. A set of cloud providers and other services from within the LS RIs has been incorporated into the EOSC Marketplace. These services were used in the Open Calls.
The project also actively partnered across EOSC through interactions with the EOSC Governance and EOSC cluster projects. The links and understanding of EOSC was furthered by the activities of the EOSC-Life translator group building a cohort of LS RI staff able to translate between the data service needs of the involved RIs and the activities implemented within EOSC-Life.
1. Publish FAIR life science data resources in EOSC:
Here the LS RI data catalogue (https://fairsharing.org/3513) was published and training and hackathons build capacity for cloud deployment of life sciences data. The data publishing and LS RI catalogue have formed the basis for future pandemic preparedness through the European COVID-19 Data Portal and the BY-COVID project, as well as supporting work towards the cancer mission in EOSC4Cancer. RO-Crate was adopted as a model for FAIR data Objects. Formal standards for Provenance Information Management (ISO 23494-1) and the Common Provenance Model (ISO 23494-2) provide a foundation for reproducibility and reusability of data within EOSC. EOSC-Life also supported the COVID-19 Data Portal (https://www.covid19dataportal.org).
2. Provide policies, guidelines and a toolkit for secure and ethical data reuse:
The EOSC-Life sensitive data toolbox helps data providers make their sensitive data available for secondary use. This includes data access procedures, requirements for hosting/distributing and access control mechanisms for sensitive data (including Access and Benefit Sharing via Nagoya Protocol).
3. Populated an ecosystem of innovative life science tools in EOSC:
EOSC-Life established a EOSC-compatible roadmap to support and guide the development of cloud-based workflows by RIs and released WorkflowHub.eu a public registry for computational workflows. The EOSC-Life tools ecosystem has been adopted within other domains, e.g environmental sciences and astronomy. The LS Login system is fully operational (https://lifescience-ri.eu/ls-login.html) and provides common authentication and authorization services for secure federated access in EOSC.
4. Enable data-driven research in Europe by connecting life scientists to EOSC via Open Calls for participation:
EOSC-Life organised Open Calls for data and user projects were successful with 11 external partnership projects selected from 91 applications. All user projects are now concluded with reports publicly available on the EOSC-Life website. Data, workflows and other digital research artefacts are deposited as FAIR digital objects in suitable repositories. A set of cloud providers and other services from within the LS RIs has been incorporated into the EOSC Marketplace. These services were used in the Open Calls.
The project also actively partnered across EOSC through interactions with the EOSC Governance and EOSC cluster projects. The links and understanding of EOSC was furthered by the activities of the EOSC-Life translator group building a cohort of LS RI staff able to translate between the data service needs of the involved RIs and the activities implemented within EOSC-Life.
EOSC-Life has fostered a significant number of data experts, tool developers and cloud engineers collaborating across LS RI to bring their data, tools and workflows into the EOSC for reuse. For instance, the trained (RP1) 32 Data experts from the 13 LS RIs have been critical in processing applications in EOSC-Life Open Calls and have been instrumental in developing the life science data catalogue in EOSC (https://fairsharing.org/3513). Collectively this group has developed best practices for long-term sustainability of data and other digital resources (https://doi.org/10.5281/zenodo.8338931) and continues to develop the joint data capabilities of Europe’s life science research infrastructures.
Unblocking the legal and administrative barriers for sharing human research data across geographical/organisational boundaries – while preserving the trust of research participants - will pave the way for continent-scale cohorts in life science research. The EOSC-Life sensitive data toolbox was launched to help data providers make their sensitive data available for secondary use. The LS Login provides a common foundation for secure federated access. In addition, EOSC-Life partners contributed to the European reference implementation of a transnational federated genome data service in the context of the GA4GH Federated Analysis Service Project.
Most importantly, the ambition to create an open, collaborative, digital space for life sciences has been realised through a reusable, and reused, toolkit. To meet the ambition on FAIR science, data and software need to be archived in online portals with annotated metadata so that they can be found and reused. One of EOSC-Life's key outcomes was to support the registration, dissemination, and application of reference collections of curated FAIR data repositories, such as those hosted by FAIRsharing.org. EOSC-Life created new standards and services to support the existence, sustainability, and exchange of provenance information, metadata, and workflows. Through the Open Calls the long-term partnerships with user communities that drive sustainability have been formed and project outcomes are being taken forward through the core operations of the LS RIs as well as a suite of new EC projects.
Unblocking the legal and administrative barriers for sharing human research data across geographical/organisational boundaries – while preserving the trust of research participants - will pave the way for continent-scale cohorts in life science research. The EOSC-Life sensitive data toolbox was launched to help data providers make their sensitive data available for secondary use. The LS Login provides a common foundation for secure federated access. In addition, EOSC-Life partners contributed to the European reference implementation of a transnational federated genome data service in the context of the GA4GH Federated Analysis Service Project.
Most importantly, the ambition to create an open, collaborative, digital space for life sciences has been realised through a reusable, and reused, toolkit. To meet the ambition on FAIR science, data and software need to be archived in online portals with annotated metadata so that they can be found and reused. One of EOSC-Life's key outcomes was to support the registration, dissemination, and application of reference collections of curated FAIR data repositories, such as those hosted by FAIRsharing.org. EOSC-Life created new standards and services to support the existence, sustainability, and exchange of provenance information, metadata, and workflows. Through the Open Calls the long-term partnerships with user communities that drive sustainability have been formed and project outcomes are being taken forward through the core operations of the LS RIs as well as a suite of new EC projects.