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BUILDING A DIGITAL �SPACE FOR THE LIFE �SCIENCES

Dr Natalie Haley, WP3 Co-Lead

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Creation of knowledge by connecting digital life science data will transform our societies and allow us to address major challenges facing humanity ��

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EOSC-Life Consortium

13 ESFRI Health and Food Research Infrastructures

47 Partners and 17 linked 3^rd parties
Sourcing e-Infrastructure services from EOSC (Cloud, AAI, … )

4 year Project, 26 M€

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EOSC-Life: an open collaborative space for digital biology in Europe�

Establish EOSC-Life by publishing FAIR life science data resources in EOSC
Provide the policies, guidelines and processes for secure and ethical data reuse
Populate an ecosystem of innovative life-science tools in EOSC
Enable data-driven research in Europe by connecting life scientists to EOSC via open calls for participation

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EOSC-Life help develop EOSC and EOSC partnership

Co-create and integrate EOSC federating core

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EOSC-Life help develop EOSC and EOSC partnership

Open Science as default –

create, adapt and adopt policies

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EOSC-Life help develop EOSC and EOSC partnership

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EOSC-Life – additional COVID-19 actions contribute to European COVID-19 Platform

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Repository for COVID-19 Clinical Trial Data

Data Integration components for European COVID-19 Data Portal - https://www.covid19dataportal.org/

COVID-19 data

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Examples of project activities relevant to the eHealth BoF

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Regulatory landscape analysis
Toolbox for sharing of sensitive data
Demonstrators and open calls in sensitive data
Training activities

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WP4 Landscape analysis

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Task 4.1 Regulatory compliance of sensitive health data and biological and medical research data management: policies, code of conduct, national implementation, de-identification

The first step of the landscape analysis (desktop research) has been concluded (D4.2).
The second step of the landscape analysis (semi-structured interview guide – national experts) is ongoing.

- National experts from 21 EU countries have been identified and contacted.

- Greece, France, Germany, Finland, Ireland, Hungary, Italy, the Netherlands, Norway, Poland, Portugal, Slovakia, Spain, Czech Republic, Belgium, Sweden, Switzerland interviews are completed/scheduled (including follow-up interviews)

Preliminary results:

research = qualitative, investigative (no single country expert has complete overview; “snowballing” between legal/ethical and technical experts to answer our questions)
national electronic health record (EHR) strategies (e.g., FI) vs. regional, scattered approaches (e.g., SE)
diverging definitions of EHR, strategy (if any, often “in the making”) vs. implementation
different speeds & priorities across Europe (e.g. north-south, genomics-in health care, EHDS)

A report will be provided and used to inform D4.5 “Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes”

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The EOSC-Life Toolbox for sensitive data sharing

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The aim of the EOSC-Life Toolbox for sensitive data sharing is to provide guidance to:

- researchers, who are sharing data or wish to share data in the future

- researchers, who are requesting data for secondary use

Scope of the Toolbox:

Only secondary use of data is considered; in case of primary use only those aspects related to future reuse of the data will be considered.

The content of the Toolbox will not be developed de novo and is driven by

1. existing data, recommendations, procedures, best practices, and links to software (tools) to support data sharing and reuse relevant for sensitive data management in a cloud environment (e.g. EOSC);

2. guidelines and other useful resources drafted in the context of EOSC-Life

The design and content is driven by 6 RIs: ECRIN, EATRIS, BBMRI, EMBRC, ERINHA, Euro-BioImaging

Where exactly we stand now: We decided that we needed to turn practical so instead of providing an additional set of recommendations for sensitive data sharing we are working on developing a toolbox that will not create resources de novo but provide pointers to guidelines/recommendations/good practices/tools already existing.

So far we have provided the general design and scope of the toolbox, a categorisation system that has been refined through a pilot study of tagging 110 resources by RI experts (and that will be the initial toolbox content) and an early demonstrator of the toolbox management of resources.

More details here:https://docs.google.com/presentation/d/1mWbG3QbHbMNR3gH_3L6NwyRa1TE06Gtz/edit#slide=id.gca5f557cbf_0_50 (e.g. the considerations of its technical implementation, process for the refinement of the categorisation system through the pilot study etc.)

There are other WP4 activities going on at the moment that can be mentioned if you see fit as « work in progress »:

- a report on data standards for observational and interventional studies, and on interoperability between healthcare and research data (Steve Canham has a presentation about this topic next week at the EATRIS Summerschool)

- a report on national health databases and registries with description of the access procedures for reuse for research purposes

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The EOSC-Life Toolbox for sensitive data sharing - status

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Categorisation system developed and approved by the participating RIs; it includes 6 dimensions: Resource types, Research fields, Data types, Stage in data sharing life cycle, Geographical scope and Specific topics.

A pilot study including tagging 110 selected resources as initial content for the toolbox is ongoing using a demonstrator developed within EOSC-Life.

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D7: Accessing human sensitive data using WfExS�(Workflow Execution Service backend, dashed lines represent ongoing or future flows)

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CWL/Nextflow engine

Inputs + Reference files

Containers

Workflow repository

Execution provenance

Launch

Materialize

(in a secure gocryptfs FUSE mount point)

Clone workflow repo or�RO-Crate workflow (raw or from WH)

or

workflow files at a GA4GH TRSv2 service

Gather

Generate from provenance

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3

2

5

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Upload

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a pair of public and private keys are generated used with Crypt4GH

...and others

Generate from inputs

https://github.com/inab/WfExS-backend�https://www.eosc-life.eu/d7/

WfExS (which could be pronounced like "why-fex", "why-fix" or "why-fixes") project aims to automate next steps:

Set up the working directory. If the work has been requested to be secured, an encrypted gocryptfs filesystem is created, and its key is encrypted using GA4GH crypt4gh.
Fetch and cache a workflow from either:

A GA4GH TRSv2-enabled WorkflowHub instance (which provides RO-Crates).
A GA4GH TRSv2 (2.0.0-beta2 or 2.0.0) enabled service. Currently tested with Dockstore and WorkflowHub in degraded mode.
A straight URL to an existing Research Object as an RO-Crate in ZIP archive describing a workflow.
A git repository (using this syntax for the URI)
A public GitHub URL (like this example).

Identify the kind of workflow.
Fetch and set up workflow execution engine (currently supported Nextflow and cwltool).
Identify the needed containers by the workflow, and fetch/cache them.
Fetch and cache the inputs (when it is allowed), represented either through an URL or a CURIE-represented PID (public persistent identifier). The sources could be under controlled-access.
Execute the workflow in the working directory (which could be encrypted).
Optionally describe the results through an RO-Crate, and upload both RO-Crate and the results elsewhere in a secure way (still being developed).

This development is relevant for projects like EOSC-Life or EJP-RD.

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~ 120 consultation requests

72 submitted proposals

70 proposals in technical evaluation

61 proposals in scientific review

15 shortlisted proposals

8 funded projects

Sept- Dec 2020

22 Dec 2020

January 2021

February 2021

March 2021

April

2021

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PID 13888 - Open Source Secure Data Infrastructure and Processes for Life Sciences (OSSDIP4LIFE)

Andreas Rauber, TU Wien, Martin Weise, Martin Krajiczek, Dietmar Winkler, Tomasz Miksa, Niki Popper�

OSSDIP is an open-source high-security data visiting platform developed by TU Wien.

In this EOSC-life project OSSDIP will be adapted to the needs of selected data owners in the life sciences, extending its functionality to support more flexible data analytics. This platform will allow data owners to provide:

highly selective access (data visiting)
to specific (fine-granular or aggregated) subsets of data
for identified individuals
for limited periods of time
to answer precisely defined questions accepted by the data owner

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Training

Webinars & e-learning

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https://www.eosc-life.eu/services/training/

E-learning under development

EOSC-Life for dummies
COVID data portal submission
Reproducibility
MICHA quick tour
Introduction to FAIR principles

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OLS-4 Timeline

Application period 15 June - 15 July 2021

OLS-4 Q&A Webinars Week of 5 July 2021

Cohort announcement mid-August 2021

OLS-4 Cohort begins mid-September 2021

OLS-4 Cohort ends January 2022

Join the program

OLS-4 period: Sep 2021 - Jan 2022

Apply individually or in team to join the cohort

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WP9 Remote training series

An informal series to support transferring face-to-face training to remote delivery

Monthly on Friday 11:00 -12:00 CET, open to all EOSC-Life RIs, ESFRI projects, e-infrastructures and their national node institutes

Shared document with announcements and upcoming topics

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Upcoming sessions:

Regular series will resume in September
02.07.2021 - 1-day workshop on hosting hybrid events (see next slide)

Planned

Accessibility Please suggest speakers and relevant topics

Previous sessions available on an unlisted YouTube playlist

Highlight useful experience with specific tools or software
Lessons learned from remote events

Always looking for speakers and suggestions for new topics!

Want to be kept informed? Email Daniel Thomas López

dthlopez@ebi.ac.uk

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EOSC-Life Hosting Hybrid events workshop

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With COVID-19 pandemic, remote events are now successfully organised, but some aspects of face-to-face events are difficult to replicate in virtual events, e.g. networking, engagement. Hybrid events could be a solution, but experience for its organisation is scarce.

Audience:

Anyone organising events; EOSC-Life beneficiaries, RIs (Hub & nodes), ESFRI cluster projects will be prioritised

Aim of the workshop:

Many organisations will out of necessity look at organising hybrid events. In this workshop we will discuss experiences, challenges and approaches that could be taken.
We hope to improve interaction among EOSC-Life RIs (hubs and nodes) when organising hybrid events

Knowledge sharing approach
Highly interactive
Check programme here
Registrations closing soon!

For questions or registration contact:

Daniel Thomas López

dthlopez@ebi.ac.uk

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Thank you!

Learn more about EOSC-Life outcomes through our….

Achievements brochure published March 2021

Achievements page on our website: eosc-life.eu/achievements

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