Handling Health Data: FAIR Research Objects for Trusted Research Environments

Trusted Research Environments (TREs) are secure locations in which data are placed for researchers to analyse. TREs can be set up to host administrative data, hospital data or any other data that needs to remain securely isolated. It is hard for a researcher to perform an analysis across multiple TREs, requesting and gathering the data needed from each one. Federated analysis widens the scope of research and makes more effective use of data, but that data needs to be analysed across geographical or governance boundaries, for example in devolved healthcare in the UK and across national borders in Europe. 

A federated infrastructure makes it much easier for analysis tools to access multiple TREs. Health Data Research UK (https://www.hdruk.ac.uk/) through its DARE UK programme (https://dareuk.org.uk/) is developing a blueprint for TRE federation [1] and tools for federated data discovery.  ELIXIR, the European Research Infrastructure for Life Science Data (https://elixir-europe.org/), has developed Federated European Genome-Phenome Archive (FEGA) [2] and services for FAIR data management and computational workflows using GA4GH standards [3].

There are different ways of implementing the well-established TREs, and many popular analysis tools already in widespread use, so solutions need to be readily adoptable by existing systems. Moreover, the infrastructure needs to work within the “Five Safes” framework [4] that aims to protect data and enable data services to provide safe research access to data. The “Five Safes RO-Crate” [5] is a new way of packaging up the digital objects needed for research requests and results with the information needed for the tools and TRE providers to ensure that the Crates are reviewed and processed according to Five Safes principles. RO-Crate [6] is a community effort to establish a lightweight, native approach to packaging research data with their metadata (https://www.researchobject.org/ro-crate/). Sponsored by ELIXIR and others, it has become a widely adopted framework for inter-service exchange, resource archiving, and reproducible reporting, used by digital research infrastructures and their services, including ELIXIR, the European Open Science Cloud, and the Australian BioCommons. It is an implementation of the FDO Forum’s FAIR Digital Objects (https://fairdo.org/).

The TRE-FX project (https://trefx.uk/) has piloted FAIR Five Safes RO-Crates and answering data queries within HDR UK TREs using pre-approved workflows using ELIXIR’s workflow execution technologies. Partnering with TREs from Scotland, Wales and England and analysis toolkits (DataSHIELD, BitFount), TRE-FX streamlines the exchange of requests and results between analysis clients and TREs while ensuring that the access is safe and the process transparent. TELEPORT (https://dareuk.org.uk/driver-project-teleport/), a sister DARE UK project, follows a complementary federation strategy of ethereal “pop-up” TREs for requests that are only feasible over combined TREs.  The combination of TRE-FX and TELEPORT is a powerful hybrid capable of addressing practical federated analysis patterns working within current data governance processes.

From March 2024 HDR-UK and ELIXIR will combine forces in the Horizon Europe EOSC-ENTRUST project which aims 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.

References

[1] DARE UK, “Federated Architecture Blueprint”, 2023, https://dareuk.org.uk/our-work/federated-architecture-blueprint/

[2] European Genome-Phenome Archive, FederatedEGA, https://ega-archive.org/federated

[3] Thorogood A et al, “International federation of genomic medicine databases using GA4GH standards”, Cell Genomics, 1(2), 2021, https://doi.org/10.1016/j.xgen.2021.100032

[4] UK Health Data Research Alliance, & NHSX. (2021). Building Trusted Research Environments - Principles and Best Practices; Towards TRE ecosystems (1.0). Zenodo. https://doi.org/10.5281/zenodo.5767586

[5] Soiland-Reyes, S., Wheater, S., Giles, T., Goble, C., & Quinlan, P. (2023). TRE-FX Technical Documentation - Five Safes RO-Crate (0.4). Zenodo. https://doi.org/10.5281/zenodo.10376350

[6] Soiland-Reyes S, Sefton P, Crosas M, Castro LJ, Coppens F, Fernández JM, Garijo D, Grüning B, Rosa ML, Leo S, Ó Carragáin E, Portier M, Trisovic A, RO-Crate Community, Groth P, Goble C (2022):
“Packaging research artefacts with RO-Crate” Data Science 5(2), https://doi.org/10.3233/DS-210053

ABOUT THE AUTHOR(S)

Carole Goble CBE FREng FBCS

Carole Goble is a Professor of Computer Science at the University of Manchester, UK. She is a leader in Digital Research Infrastructures, translating technical innovations in distributed computing, semantic and metadata technologies, data and software sharing and computational workflows into FAIR and Open information solutions for scientists, in particular the Life Sciences and Biodiversity. She is currently: Joint Head of Node of ELIXIR-UK the UK node of ELIXIR, the European Research Infrastructure for Life Science Data; joint lead of the Federated Analytics programme for Health Data Research UK and a founder of the UK’s Software Sustainability Institute. Carole is an author of the seminal FAIR principles for scientific data and recipient of the Microsoft Jim Gray award for her contributions to eScience.