HealthData@EU Pilot concludes with full deliverables, advancing EHDS infrastructure for secondary data use

The HealthData@EU Pilot project has concluded with the release of all final deliverables, marking a major step in building the European Health Data Space (EHDS) infrastructure to enable secure, cross-border secondary use of health data.

Over the course of 27 months, the project brought together 17 partners from across Europe to develop and evaluate a cross-border digital infrastructure. The goal was to enable secure, interoperable access to health data for research, innovation, policymaking, and regulation. As the project concluded, its final outputs were recognized as a significant milestone:

“These deliverables mark a crucial step toward the realization of a the EHDS infrastructure, ensuring harmonized data governance, technical alignment, and legal clarity for the secondary use of health data across Europe.”

Core deliverables support EHDS implementation

The HealthData@EU Pilot produced outputs across all major areas required for EHDS infrastructure development. These include technical, legal, and organizational building blocks:

• A full IT architecture framework (WP5), including a Minimum Viable Product deployed in France, Denmark, and Finland.
• A health-specific extension of DCAT-AP, HealthDCAT-AP, to improve metadata quality, findability, and reuse of health data (WP6).
• Legal tools, including a common data access application form and guidance on de-identification, secure transfer, and data permit procedures (WP7).
• Technical recommendations on data interoperability, quality assurance, and privacy-enhancing technologies (WP8).
• Practical advice on setting up Health Data Access Bodies (HDABs), including staffing, governance, IT deployment, and use of HealthDCAT-AP and common access forms (WP4).

As noted in Deliverable D4.1:

“Key recommendations include hiring skilled personnel, deploying national IT components, implementing a standardized metadata catalogue using HealthDCAT-AP, and utilizing common data access forms to streamline data requests.”

Evaluation confirms project impact and highlights key challenges

Deliverable D3.1, the Evaluation Report, provides a comprehensive analysis of the HealthData@EU Pilot project’s implementation and outcomes. The report assessed progress across all work packages using predefined Key Performance Indicators and incorporated feedback gathered through structured questionnaires and interviews with project partners.

As noted in the report,

“The report offers a comprehensive overview of the HealthData@EU pilot project, which started on 1 October 2022 with a duration of 27 months.”

The project’s dual aims were to build and deploy an IT infrastructure for secondary health data use and to test its feasibility through five multi-country use cases. These included studies on cardiovascular risk prediction, COVID-19 outcomes in vulnerable populations, antimicrobial resistance surveillance, and genomic signatures in colorectal cancer.

The report identifies persistent challenges to the secondary use of health data, including legal fragmentation, security concerns, interoperability gaps, and confirms that HealthData@EU has made tangible progress toward addressing them:

“The secondary use of health data involves harnessing data from various population-level sources […] to enhance personal care planning, medicine development, safety monitoring, research, and policymaking.”

Importantly, the project’s outputs informed the finalization of the EHDS Regulation, particularly Chapter IV, which outlines rules and conditions for cross-border secondary data use.

Lessons learned for future EHDS projects

While the pilot successfully delivered all planned outputs, the evaluation highlights several lessons for future EU-level digital health initiatives. These include:

• The need for stronger project management and agile delivery methods.
• Greater coordination between work packages and stakeholders, including through informal and in-person meetings.
• More robust integration of legal, technical, and scientific perspectives.
• Dedicated communication roles and adequate dissemination budgets.
• Strategic planning to ensure sustainability beyond the funding period.

The importance of continuity was emphasized in the report’s recommendation to:

“Ensure smooth communication and handover between coordinators of successive projects and actions related to the secondary use of health data.”

Navigating regulatory uncertainty was also a notable challenge. As the WP7 lead observed,

“The moving target of the EHDS regulation, including delays in the regulation and changes to the entire framework, has made it complicated to achieve concrete advances.”

Nevertheless, strong collaboration with the European Commission and HaDEA played a critical role in overcoming these difficulties.

A reference model for national and EU implementation

The completion of the HealthData@EU Pilot provides a tested blueprint for Member States and EU institutions as they move toward implementing the EHDS Regulation. By demonstrating the feasibility of a federated data infrastructure, the project highlights the technical, legal, and organizational conditions necessary for scaling secure, cross-border secondary use of health data.

Central to this effort is public confidence in the system. As the evaluation notes,

“Public trust and transparent communication are deemed crucial for the success of the EHDS.”

With all deliverables now publicly accessible, the project offers practical tools, standards, and governance recommendations that will support a harmonized approach to health data use across Europe.