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Providing an open collaborative space for digital biology in Europe

Periodic Reporting for period 1 - EOSC-Life (Providing an open collaborative space for digital biology in Europe)

Reporting period: 2019-03-01 to 2020-08-31

Advances in research technology have led to a vast increase in data volumes produced by life science research. These datasets are beyond what can be handled, shared and analysed using classical tools and often contain treasure troves of data beyond what was analysed in 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 of individual projects.
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. We do this by publishing our data as FAIR Data Resources, linking reusable tools and workflows to standardised computing services in national life-science clouds, connecting our users across Europe to a single login authentication and resource authorisation system, and developing the data policies needed to preserve and deepen the trust given by research participants and patients volunteering their data and samples.
EOSC-Life delivers its vision through three specific project objectives:
1. Establish EOSC-Life by publishing FAIR life science data resources for cloud use
2. Create an ecosystem of innovative life-science tools in EOSC
3. Enable ground-breaking data driven research in Europe by connecting life scientists to EOSC
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, and the resulting data will be openly accessible for reuse through the European Open Science Cloud in full compliance with all ethical, regulatory and legal requirements.
Significant progress was made toward the overall project objectives in all work packages (WPs). Importantly, even though the coronavirus pandemic caused delays in specific deliverables, overall the EOSC-Life beneficiaries were able to pivot to provide important services to researchers of COVID-19 through initiatives like the COVID-19 Biohackathon, accelerate the delivery of key components for COVID-19 research (e.g. workflowhub.eu released 12 months ahead of schedule) and development of 2 new WPs for COVID-19 data integration and clinical trials in response to EC and ERA requests.
WP1 has engaged with the demonstrator projects to assess their needs, delivering an evaluation of needs and strategies for cloud deployment based on WP3 demonstrators and shaping WP1 and WP3 future project cloud developments. We have delivered training and followed up with a hackathon addressing cloud deployment for life sciences data repositories. The impact of this work was a set of assessment criteria for the demonstrators.
WP2 defined a EOSC-compatible roadmap to support and guide the development of workflows by RIs and the WP3 demonstrator projects. It launched the WorkflowHub.eu a public registry for computational workflows.
WP3: The first pilot projects (“Demonstrators”) started and WP3 matched demonstrators and WP1/WP2 data experts and tool developers to help with the projects. To define the planned Open Calls, WP3 delivered an internal project scoping exercise, then produced guidelines and examples for applicants.
WP4: The landscape analysis of national legal and ethical requirements describe different national strategies and focus areas for EOSC (D4.2). Thematic workshops on FAIR, pseudo/anonymisation, case studies, and the Nagoya Protocol identified solutions for the interdisciplinary needs and federated environments.
WP5: The technical and non-technical requirements of Life Science (LS) AAI were collected and published in D5.1. Work has started to deploy the LS AAI with e-infrastructures.
WP6 supported the implementation of the FAIR principles across the LS RIs and released a machine-actionable provenance model to manage reproducibility and reusability for data and biological materials.
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. First scientific use cases were selected and deployed to the cloud services.
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 analysed our training needs and designed questionnaires to assess the long-term impact of EOSC-Life training activities. The first training open call cycle was concluded and first training activities performed.
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). The first review was executed at the 1st Annual General Meeting, 3/4 March 2020.
WP13 helped launch the COVID-19 Data Portal, a component of the European COVID-19 Data Platform, providing free and open access to data from ca. 16 biomolecular data resources. Offering ca. 150,000 records, the system provides a key foundation for COVID-19 research.
WP14 defined the high-level concept of the repository for individual participant data (IPD) from COVID-19 trials. This includes 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.
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 example, in April 2020 EOSC-Life supported The International COVID-19 Biohackathon, demonstrating the power of this idea and highlighting many of the issues that now need to be addressed during the remainder of this project to move beyond powerful demonstrators to routine provisioning.
Unblocking the legal and administrative barriers for sharing human research data across geographical and organisational boundaries – while preserving the trust of research participants - will pave the way for continent- scale cohorts in life science research. In the first 18 months EOSC-Life has delivered a comprehensive mapping of national requirements for sharing sensitive data and built on these efforts to rapidly establish requirements - with broad stakeholder input - for a COVID-19 clinical trial data repository. 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