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Providing an open collaborative space for digital biology in Europe

Periodic Reporting for period 2 - EOSC-Life (Providing an open collaborative space for digital biology in Europe)

Reporting period: 2020-09-01 to 2022-02-28

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 these datasets sparks data-driven research beyond the initial project. Making available data, tools and workflows in the cloud is therefore necessary in order to use the data produced to the fullest extent, both within and beyond the original intended scope.

In EOSC-Life the 13 Life Science Research Infrastructures (LS RIs) in Europe create an open, collaborative digital space for life science in the European Open Science Cloud (EOSC). 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 is connecting users across Europe to a single login authentication and resource authorisation system (LS Login), and developing 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 in full compliance with all ethical, regulatory and legal requirements.
Significant progress was made toward the overall project objectives in all work packages (WPs). In addition, EOSC-Life was able to provide important services to researchers of COVID-19 with 2 new WPs for COVID-19 data integration and clinical trials in response to EC/ERA requests.
- WP1 has published and extended the LS RI data catalogue (https://fairsharing.org/3513) engaged with Open Call user projects to assess their needs, resulting in an evaluation of needs and strategies for cloud deployment and delivered training/a hackathon addressing cloud deployment for life sciences data repositories.
- WP2 started a EOSC-compatible roadmap to support and guide the development of cloud-based workflows by RIs and the WP3 projects, including further development of WorkflowHub.eu a public registry for computational workflows and the LifeMonitor benchmarking tool. The EOSC-Life tools ecosystem has been adopted within other domains.
- WP3: The EOSC-Life Open Calls for user projects were successful with 11 external partnership projects selected from 91 applications. All user projects are now launched and teams formed with the EOSC-Life WPs.
- WP4: Building on the landscape analysis of national legal and ethical requirements for data sharing, a first version of the EOSC-Life sensitive data toolbox was launched to help data providers make their sensitive data available for secondary use. A review of data standards in healthcare and interventional and observational research was done, their interoperability explored, an inventory taken of national health databases, registries and their data access procedures, requirements for hosting/distributing and access control mechanisms for sensitive data (Nagoya protocol, Access and Benefit Sharing) listed.
- WP5: Technical/non-technical requirements of LS AAI were collected and published in D5.1/5.3. 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.
- WP6 supports the implementation of FAIR principles across the LS RIs. RO-Crate has been adopted as a model for FAIR data Objects in EOSC-Life. Advancing formal standards for Provenance Information Management (ISO 23494-1) and the Common Provenance Model (ISO 23494-2) provides a robust foundation to manage reproducibility and reusability for data and biological materials within EOSC.
- WP7 established a Resource Allocation Process for provision of cloud resources to project activities. An initial set of cloud providers from within the LS RIs has been incorporated into the EOSC Marketplace. These services were used in the Open Calls.
- WP8 established interactions with the EOSC Governance and EOSC cluster projects, leading to a coordinated input from clusters to the activities of the EOSC Executive Board and the EB Work groups. It also worked on a framework to assess the reproducibility and impact of the open life science data provided by EOSC-Life.
- WP9: Based on analysis of LS RI training needs, remote training was delivered against a range of topics (data resources, cloud deployment, etc). In addition WP9 orchestrated the activities of the EOSC-Life “translator group”, fostering a cohort of LS RI staff able to translate between the data service needs of the involved RIs and the activities implemented within the WPs.
- WP10 delivered the Communication Plan, project branding, and stakeholder analysis. The website, newsletter and social media accounts have updated stakeholders on project outputs. WP10 disseminated other WPs’ activities and engaged infrastructure users.
- WP11 has established effective links to project management staff in all RIs and has supported the smooth running of the project. It delivered the data management plan, the Consortium Agreement and established the project governance including the Scientific and Ethics Advisory Board (SEAB) and oversaw a successful Midterm review.
- WP13 supports the COVID-19 Data Portal (https://www.covid19dataportal.org) a component of the European COVID-19 Data Platform, providing free and open access to data from 21 biomolecular data resources. A country-by-country campaign to assist scientists sequencing SARS-CoV-2 and working on patient-related data sets to make their data available in, and/or link to, the COVID-19 Data Portal has yielded a deep and rich viral data set. Offering by the end of February 2022 over 13,000,000 records, the system continues to provide a key foundation for COVID-19 research.
- WP14 has delivered a high level description of the COVID-19 repository, covering the legal context of data object sharing in COVID-19 research, functional specification, quality assurance, implementation plan, sustainability and governance, evaluation of routine use and impact, usability and user friendliness, outreach, partnerships and scalability. A partnership with VACCELERATE is underway.
EOSC-Life will foster 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 re-use. For instance, the trained (RP1) 32 Data experts from the 13LS 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).
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.
EOSC-Life: A schematic view