DARE-FX: Delivering a federated network of TREs to enable safe analytics

Lead Research Organisation: The University of Manchester
Department Name: UNLISTED

Abstract

Trusted Research Environments (TREs) are secure locations in which data are placed
for researchers to analyse. They host administrative data, hospital data or any other
data that must be securely isolated and only accessible for approved queries by
approved researchers. However, it is hard for a researcher to perform analysis across
multiple TREs, for example when data is to be analysed across geographical or
governance boundaries, such as the devolved nature of healthcare in the United
Kingdom. Yet this ability is urgently needed. Analysis across a federation of TREs
would enable timely analysis of UK wide scattered data to answer urgent questions,
as we needed in the COVID-19 pandemic.

The technologies and standards we need to be able to do this are available now. They
do not need to be invented. DARE-FX is assembling leading technology providers from
ELIXIR-UK and HDR-UK, with three TRE providers and two leading analysis platforms
to show through a real reference implementation how we can use secure Research
Objects to move between TREs while still supporting the Five Safes principles that
govern and protect patient data; all overseen by patient representatives.

The impact will be a step change for how researchers can safely combine data from
many sources, and for how data providers from any sector can safely implement this
using technology and standards we already have today.

Technical Summary

Background
The main concept of a Trusted Research Environment is that data remains within the
secure boundaries of a technical and governance wrapper, to enable analysis in
accordance with the Five Safes principles (Safe People, Project, Data, Settings,
Outputs). Yet researchers need to perform analysis across multiple TREs that may
also span traditional funder silos: across multiple geographical locations; when some
data exists in one TRE and other data in another. When analytics are federated,
queries are pulled into the TREs containing the data, then processed and the results
returned subject to disclosure checking, without the data leaving the TREs.

Currently TREs do not have an effective approach to standardise the transfer of
information in and out of their environments or a common approach to controlling how
analyses are deployed and run. A framework is needed to ensure that federated
analytic queries run on TREs across the UKRI and ADR-UK networks are
interoperable, reusable and auditable to the Five Safes. Such a potential framework
has been developed by ELIXIR-UK, the national node for the European Research
Infrastructure for Life Science Data, and pre-piloted by the FED-NET TRE.

By using existing tooling and open standards within a Service-API driven architecture,
DARE-FX aims to demonstrate an exemplar framework and reference implementation
for federated analytic queries that enables Five Safes analytics over a federated
network of UK TREs. The framework and reference implementation will be developed
with PPIE as full team members.

Methods
We have gathered expertise from across the UK, including three different kinds of
TREs from HDR-UK/ADR-UK (UKSerp/SAIL, TREEHOOSE, PIONEER), pre-existing
federated analytic services (DataShield, BitFount), and ELIXIR’s interoperability
technology (workflow execution, RO-Crate Research Objects). The project includes
partners from previous DARE UK projects: FAIR TREATMENT, TREEHOOSE and
FED-NET. This expert team will assemble a core set of federated services that
demonstrate how existing tooling and open standards can be used to create a Five
Safes RO-Crate framework that adheres to the HDR-UK Five Safes model and will
thus ensure public trust.

To prove cross council utility across research domains and sectors we will collaborate
with the TRE providers SAIL, FED-NET and HIC to deliver a open-source reference
implementation that interfaces with the existing federated analytic services
DataSHIELD (to allow querying of ONS administrative data) and a commercial partner
Bitfount (to enable querying of healthcare data). An ELIXIR sponsored workshop has
already been conducted to explore the proposed concepts and implementation with
all partners.

To ensure our implementation is open for public scrutiny we will deliver a whitepaper
based on our framework, publicly available Bitfount and DataSHIELD federated
analytic workflows, an integration with the HDR data use registry and a publication
detailing the implementation. All results will be open source.
 
Description EOSC-ENTRUST: A European Network of TRUSTed research environments
Amount £155,659 (GBP)
Funding ID 10104655 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 03/2024 
End 02/2027
 
Description MIREDA (Mother and Infant Research Electronic Data Analysis) Partnership
Amount £1,236,698 (GBP)
Funding ID MR/X02055X/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 06/2023 
End 06/2026
 
Title Five Safes RO-Crate 
Description Five Safes RO-Crates enable the exchange of query requests and results between analysis clients and TREs while ensuring that the access is safe and the process transparent. Included within its specification are eight steps that ensure that the RO-Crate's metadata for safe data, safe people, safe projects, safe settings and safe outputs are reviewed according to Five Safes principles. 
Type Of Material Improvements to research infrastructure 
Year Produced 2023 
Provided To Others? Yes  
Impact It is to be used in the HDR UK QQ2 Federated Analytics workstream and the EOSC-ENTRUST EU Horizon Europe project to create a European network of trusted research environments for sensitive data and to drive European interoperability by joint development of a common blueprint for federated data access and analysis. 
URL https://trefx.uk/5s-crate/
 
Description ELIXIR Workflow Execution Service 
Organisation Barcelona Supercomputing Center
Country Spain 
Sector Public 
PI Contribution The ELIXIR WfExS develpoed by the Barcelona Supercomputing Centeris used by the TRE-FX project to execute workflows in TREs.
Collaborator Contribution They contributed the WfExS and made revisions
Impact The EU Project EOSC-ENTRUST - https://eosc-entrust.eu/, starting 2024. The WfExS Partners in Barcelona and the TRE-FX project partners will work together on federated analytics development using workflows and the Five Safes RO-Crate
Start Year 2023
 
Description Research Object 
Organisation researchobject.org
Sector Charity/Non Profit 
PI Contribution researchobject.org is a grass roots community to develop and disseminate Research Objects, their concept, adoption, and other latest developments. It was established by Prof Goble's e-Science group and is now a global community with academic and commercial members.
Collaborator Contribution The community have developed specifications, implementations and run a series of international workshops.
Impact Specifications of Research Objects, including RO-Crate http://www.researchobject.org/2019-11-15-ro-crate-1-0/ funding from Elsevier, incorporation into data repositories (DataVerse, Mendeley Data) and the NIH Data Commons Core to the development of the workflow collaboratory for the EOSCLife project (European Open Science Cloud Life). A component of the EU EOSC FAIR Digital Object Framework Multidisciplinary - chiefly the life sciences, biodiversity and computer science
Start Year 2013
 
Title HDR Cohort Discovery / TRE-FX / RQuest integration 
Description It allows compatibility between the work of TRE-FX, the HDR Programme (Cohort Discovery) and BC Platforms software 
Type Of Technology Software 
Year Produced 2023 
Open Source License? Yes  
Impact Now being assessed for use in the NHS England SDE Programme 
URL https://github.com/Health-Informatics-UoN/rquest-tools
 
Title Workflow for RQuest integration 
Description It is the workflow to process an HDR Cohort Discovery tool query 
Type Of Technology Software 
Year Produced 2023 
Open Source License? Yes  
Impact Forms part of the work with NHS SDE Programme and HDR Programme 
URL https://workflowhub.eu/workflows/471
 
Description BC Platforms Event in Singapore 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact International meeting to hear about our work and to create further collaborations
Year(s) Of Engagement Activity 2023
 
Description BY-COVID Project Joint Federated Analytics Workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact BY-COVID is the European Horizon Europe project for "BeYond COVID: pandemic preparedness. The TRE-FX approach for federated analytics and RO-Crates is being developed as a demonstrator for the Federated Analytics task
Year(s) Of Engagement Activity 2023
URL https://by-covid.org/
 
Description ELIXIR Bioinformatics Industry Forum 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ELIXIR Bioinformatics Industry Forum 2023, 2023-11-21, London, invited speaker, round table representation
The annual ELIXIR Bioinformatics Industry Forum was a one-day event that brings together bioinformaticians and technical specialists to explore solutions to major challenges in the data-driven life science sector.

the Forum theme was "Trusted research environments for sensitive data in the life sciences". The programme features a variety of presentations from industry and academia, offering the participants a chance to learn more about relevant initiatives and research breakthroughs in the area of TREs. The forum aimed to stimulate discussions among solution providers and enable potential collaborations.
Year(s) Of Engagement Activity 2023
URL https://elixir-europe.org/events/elixir-bioinformatics-industry-forum-2023
 
Description Federated Learning Workshop: Share the Code 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact International workshop to develop common understandings for the deployment of federated learning tools.
Year(s) Of Engagement Activity 2023
 
Description HPC-AI Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Emily Jefferson (CTO, HDR UK and Interim Director of DARE UK) was an invited speaker at the 5th Annual HPC-AI Advisory Council UK Conference. Presentation: TREs at Scale.
Year(s) Of Engagement Activity 2023
URL https://www.hpcwire.com/off-the-wire/5th-annual-hpc-ai-advisory-council-uk-conference-set-for-octobe...
 
Description Invited Seminar The University of Auckland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited talk, strong collaboration now with Center for eResearch and their TRE team
Year(s) Of Engagement Activity 2024
 
Description Invited speaker: HDR Technology Ecosystem and the Gateway: UKRI Data Infrastructure Club Show and Tell 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Emily Jefferson was an invited speaker, leading a presentation on the HDR UK Technology Ecosystem and the Gateway at the UKRI Data Infrastructure Club Show and Tell: 31st Jan 2023.
Year(s) Of Engagement Activity 2023
 
Description Invited speaker: HDR Technology Ecosystem. UK DRI Informatics Scoping Event - London. 8th and 9th March 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Emily Jefferson, CTO of HDR UK was an invited speaker to lead a presentation on the HDR Technology Ecosystem at the UK DRI Informatics Scoping Event - London. 8th and 9th March 2023
Year(s) Of Engagement Activity 2023
 
Description Invited speaker: Technology Ecosystem - Launch. Technology Ecosystem Conference/Workshop. Birmingham. 6th Feb 2023 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Technology Ecosystem Conference (6th February 2023) brought together different technology groups from across the community to strengthen relationships and generate ideas to deliver trustworthy infrastructure and services across the health data research ecosystem
Year(s) Of Engagement Activity 2023
 
Description Invited speaker: The power of DRI: A health data perspective. UKRI Digital Research Infrastructure (DRI) Congress. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Emily Jefferson was an invited speaker to present on: The power of DRI: A health data perspective at the UKRI Digital Research Infrastructure (DRI) Congress. 6th and 7th March 2023.
Year(s) Of Engagement Activity 2023
 
Description Invited talk at ELIXIR All Hands meeting 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ELIXIR is the European Research Infrastructure for Life Science Data. The All Hands attracts 400 delegates. Presented invited talk Human Genomics and Translational Data 2024-28 symposium
Year(s) Of Engagement Activity 2023
URL https://elixir-events.eventscase.com/EN/elixirallhands2023/Agenda
 
Description Japan Association for Medical Informatics Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Emily Jefferson (CTO, HDR UK and Interim Director of DARE UK) was a keynote speaker at the 43rd Joint Conference on Medical Informatics. Presentation: The UK's progress towards enabling secure, researcher access to sensitive health data at a UK population scale.
Year(s) Of Engagement Activity 2023
URL https://confit-atlas-jp.translate.goog/guide/event/jcmi2023/session/3A11-13/detail?_x_tr_sl=ja&_x_tr...
 
Description Keynote eResearch New Zealand 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote at the eResearch Conference New Zealand 2024 https://eresearchnz.co.nz/. Developed links with New Zealand and Australian eResearch communities; several sessions discussed Trusted Research Environments and sensitive data.
Year(s) Of Engagement Activity 2024
URL https://eresearchnz.co.nz/
 
Description Keynote speaker: Towards Federated Analytics for Population Data. International Data Science Conference - Tokyo, Japan, 22/05/23 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Emily Jefferson was invited as a keynote speaker to present 'Towards Federated Analytics for Population Data. International Data Science Conference - Tokyo, Japan' on 22/05/23
Year(s) Of Engagement Activity 2023
 
Description Keynote speaker: Towards Federated Analytics for Population Data. Precision Medicine & Real-World Data Conference - Singapore, 23/05/23 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Key note speaker, presented on experiences enabling a new UK infrastructure for finding and accessing population-wide data for research and public health analysis
Year(s) Of Engagement Activity 2023
URL https://info.bcplatforms.com/precision-medicine-and-rwd-conference-singapore-2023
 
Description Public Involvement and Engagement Video: Using Digital Boxes for Safe and Secure Federated Analytics 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Public Involvement and Engagement Video: Using Digital Boxes for Safe and Secure Federated Analytics to inform. Developed by the PIE activity of the award
Year(s) Of Engagement Activity 2024
URL https://www.youtube.com/watch?v=eR-6GjM6gz8
 
Description Public Involvement and engagement Video: The Federated Approach 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A PIE video to describe Federated Analytics across TREs. Developed by the PIE team of the award
Year(s) Of Engagement Activity 2024
URL https://www.youtube.com/watch?v=31AqEu3Qe1g
 
Description Research Software Engineers (RSE) Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Emily Jefferson (CTO, HDR UK and Interim Director of DARE UK) was an invited speaker to the Seventh Annual Research Software Engineering Conference. Presentation: Can convening a Technology Ecosystem help TREs to work together?
Year(s) Of Engagement Activity 2023
URL https://rsecon23.society-rse.org/
 
Description UK TRE Community Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Emily Jefferson (CTO, HDR UK and Interim Director of DARE UK) was the keynote speaker at the UK TRE Community Meeting that was part of the RSE Conference. Presentation: Call to action!
Year(s) Of Engagement Activity 2023
URL https://www.eventbrite.com/e/uk-tre-community-september-meeting-tickets-676066472017
 
Description UK TRE Satellite Workshop at RSECon 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation at RSECon2024 satellite Trusted Research Environments Satellite Meeting https://rsecon23.society-rse.org/satellite-events/
Year(s) Of Engagement Activity 2023
URL https://rsecon23.society-rse.org/satellite-events/