CZECH–SWISS COOPERATION PROGRAMME 2026–2028
Swiss–Czech Partnership for Integrating Molecular, Pathogen And Clinical Data with AI Technologies
Duration: 1 January 2026 – 31 December 2028 Budget: CZK 69 464 294 Project ID: 8K0205
ABOUT THE PROJECT
Connecting AI and Life Science Data Across Europe
Life sciences are increasingly relying on sophisticated data-driven approaches, including artificial intelligence (AI), to address challenges in public health, personalised medicine and biological research. However, progress is held back by fragmented data, limited integration of specialised datasets and computational methods, and restricted access to sensitive health information.
ELIXIR IMPACT addresses these challenges by bringing together the internationally recognised expertise of ELIXIR Czech Republic (led by IOCB Prague) and ELIXIR Switzerland (led by SIB Swiss Institute of Bioinformatics, Lausanne). Together, we are building a robust platform that integrates molecular, metabolic and clinical data with state-of-the-art AI technologies.
The project places special emphasis on developing methods and tools for data interoperability, secure sharing of sensitive information, and the application of AI in clinical and biomedical practice. Its successful implementation will strengthen the leading role of both Czechia and Switzerland in the European Research Area.
PROJECT FACTS
Basic Information
| Full title | Swiss–Czech Partnership for Integrating Molecular, Pathogen And Clinical Data with AI Technologies |
| Acronym | ELIXIR IMPACT |
| Project ID | 8K0205 |
| Call | 8K2502 – Czech–Swiss Cooperation in Research Infrastructures |
| Programme | Czech–Swiss Cooperation Programme |
| Duration | 1 January 2026 – 31 December 2028 (36 months) |
| Total budget | CZK 69 464 294 |
| Swiss contribution (85 %) | CZK 59 044 650 |
| Czech co-funding (15 %) | CZK 10 419 644 |
| Funder | Ministry of Education, Youth and Sports of the Czech Republic (MŠMT ČR) |
| Czech lead institution | Institute of Organic Chemistry and Biochemistry, CAS (IOCB Prague) |
| Swiss partner | SIB Swiss Institute of Bioinformatics, Lausanne |
| Principal Investigator | Prof. RNDr. Jiří Vondrášek, CSc. (IOCB Prague) |
| Contact | elixir@uochb.cas.cz |
PROJECT OBJECTIVES
What We Aim to Achieve
The overall aim of ELIXIR IMPACT is to significantly advance the integration and use of biological data through state-of-the-art AI approaches, creating new opportunities for research and applications in biology, personalised medicine and public health. Specifically, the project aims to:
- AI-powered data interoperability
Improve the interoperability and usability of key data resources on molecules, lipids, metabolites and pathogens through advanced semantic integration and AI-based knowledge graphs, enabling seamless access to integrated data for biomedical discovery.
- Natural language AI tools and services
Develop innovative AI-based tools and services, including natural language query systems, that improve data findability and accelerate research outcomes — making biological datasets easily usable for researchers and clinicians alike.
- Secure federated infrastructure
Create a secure and scalable computing infrastructure enabling safe sharing and analysis of sensitive omics data across borders, in line with European-level initiatives and regulatory frameworks, supporting international collaboration in clinical research and public health.
- Capacity building through training
Expand research capacity and expertise through targeted training activities, workshops and educational materials equipping researchers with practical skills in data interoperability, AI methods and secure management of sensitive data.
- Czech–Swiss scientific collaboration
Strengthen the Czech–Swiss scientific partnership by leveraging the complementary expertise, infrastructure and strategic position of ELIXIR CZ and ELIXIR CH, ensuring sustainable leadership within the European Research Area in life sciences.
SCIENTIFIC PROGRAMME
Work Packages
The project is structured into six interconnected work packages, ranging from molecular data integration and AI-powered pathogen portals to semantic interoperability, federated infrastructure, training and coordination. Each WP feeds into the others, creating a coherent ecosystem of tools, data and skills.
| WP1 | Unification of Small-Molecule Data Resources |
| Leads: Karel Berka (UPOL, CZ) · Alan Bridge (SIB, CH) |
Creates a standardised, interoperable and semantically integrated knowledge network for small molecules and their interactions in biological systems. Connects world-class resources from ELIXIR CZ and ELIXIR CH — UniProtKB, Rhea, SwissLipids, MolMeDB, ChannelsDB and IDSM — into a federated knowledge graph ready for AI-powered biomedical computation.
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| WP2 | AI-Enhanced Pathogen Portals and Public Health |
| Leads: Robert Pergl (ČVUT, CZ) · Aitana Neves (SIB, CH) · Jan Pačes (IMG ASCR, CZ) |
Strengthens capacities for sharing and analysing pathogen data to support One Health research. Delivers a new Czech Pathogen Portal as a national data node, expands the Swiss Pathogen Portal with One Health guidance, and develops LLM-powered tools for data management planning (DMP) and cross-border pathogen data sharing. • Czech Pathogen Portal — national node for pathogen data (built on virus.img.cas.cz)
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| WP3 | AI-Supported Semantic Database Integration |
| Leads: Jakub Galgonek (IOCB, CZ) · Ana Claudia Sima (SIB, CH) |
Tackles the interoperability challenge at scale by developing harmonised services enabling cross-institutional querying of SIB and IOCB knowledge graphs. Introduces natural language access to biological data and AI-driven optimisation of cross-institutional data discovery — establishing a model for the wider ELIXIR network.
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| WP4 | Federated Infrastructure for Sensitive Clinical Omics Data |
| Leads: Vojtěch Bystrý & Lukáš Hejtmánek (MU/CESNET, CZ) · Owen Appleton (SIB, CH) |
Bridges critical gaps in European federated data ecosystems by building a bilateral Czech–Swiss prototype for secure cross-border analysis of sensitive omics data. Builds on both countries’ experience in GDI, Federated EGA and EOSC ENTRUST — ensuring sensitive data never leaves its country of origin.
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| WP5 | Training and Capacity Building |
| Leads: Vojtěch Spiwok (UCT Prague, CZ) · Geert van Geest & Patricia Palagi (SIB, CH) |
Converts technical outputs of WP1–WP4 into targeted training modules, workshops and educational materials. Participants learn to run semantic queries on enriched molecular datasets, work with pathogen portals, and perform secure analyses in federated environments. AI agents are explored as tools to scale training delivery across Europe.
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| WP6 | Project Coordination and European Alignment |
| Leads: Jiří Vondrášek (IOCB Prague, CZ) |
Ensures all work packages function as a coherent whole aligned with ELIXIR’s strategic priorities and European initiatives (EOSC, GDI, FEGA). Coordinates cross-WP integration, stakeholder engagement at national and European levels, dissemination of results, and monitoring of impact metrics throughout the project lifecycle.
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PROJECT TIMELINE
Milestones and Key Deliverables
Year 1 — 2026: Foundations
Launch of all work packages, kick-off meeting between IOCB Prague and SIB Lausanne. WP1: SwissLipids RDF enrichment and ChannelsDB mapping completed (M12). WP2: Czech Pathogen Portal v2 launched (M12). WP3: Harmonised federated SPARQL services operational. WP5: First training modules delivered.
Year 2 — 2027: Integration and AI Services
WP1: MolMeDB–SwissLipids integration complete (M24); SPARQL interface extended. WP2: Swiss Portal LLM extension in progress (M34). WP3: Natural language data access live. WP4: Bilateral federated infrastructure prototype deployed; first cross-border TRE operational.
Year 3 — 2028: Consolidation, Impact and Close
WP1: IDSM fully integrating all datasets (M30–31); query catalogues published (M36). WP3: Complete cross-institutional query catalogue delivered. WP4: Federated TRE fully operational with secured omics datasets. WP5: Full training programme with AI-agent tools and online library. Final reporting and impact assessment: December 2028.
EXPECTED IMPACT
Why ELIXIR IMPACT Matters
The project is strategically timed to exploit current advances in AI that open entirely new approaches to data integration and cross-border data sharing — critical for personalised healthcare and public health. It is aligned with the EOSC initiative and strengthens the leading role of both Czech and Swiss partners in the competitive European research environment.
🏥 Better Public Health
Accelerates research on infectious diseases and the capacity to respond to outbreaks through secure, cross-border sharing and analysis of sensitive clinical and pathogen data. Contributes directly to Europe’s pandemic preparedness and One Health research.
🔬 Personalised Medicine
Supports targeted treatment approaches through deeper understanding of small molecules and metabolic processes in human health. Integrates molecular, lipid and omics data to power the next generation of precision medicine research.
🌍 European Leadership in Data Governance
Strengthens the leading role of Czech and Swiss research infrastructures in AI-driven biological data management. Contributes reusable models, tools and standards to the broader ELIXIR, EOSC and 1+MG communities.
🎓 Research Community Empowerment
Equips thousands of life-science researchers across Europe with practical skills in AI, data interoperability and secure data management. Targeted training bridges the gap between infrastructure development and everyday research use.
EUROPEAN CONTEXT
Aligned with European Initiatives
ELIXIR IMPACT directly contributes to and builds on the following European strategic initiatives:
- EOSC (European Open Science Cloud) — open, federated research data infrastructure
- GDI (Global Data Infrastructure) — genomic data access and governance
- Federated EGA (FEGA) — secure distributed archives for sensitive omics data
- EHDS (European Health Data Space) — cross-border health data sharing
- 1+MG (1+ Million Genomes) — flagship European genomics initiative
- EOSC ENTRUST — trusted research environments for sensitive data
CONSORTIUM
Partners and Team
Core Partners
IOCB Prague Ústav organické chemie a biochemie AV ČR, v.v.i. Czech Lead · ELIXIR CZ | SIB Swiss Institute of Bioinformatics Lausanne, Switzerland Swiss Lead · ELIXIR CH |
Czech Consortium Members
| IOCB Prague (ÚOCHB) | WP1 (semantic integration), WP3, WP6 — Principal investigator: Prof. Jiří Vondrášek |
| Palacký University Olomouc (UPOL) | WP1 — MolMeDB, ChannelsDB; lead: Karel Berka |
| Czech Technical University Prague (ČVUT) | WP2 — Data management planning; lead: Robert Pergl |
| Institute of Molecular Genetics, CAS (IMG) | WP2 — Czech Pathogen Portal; lead: Jan Pačes, Michal Kolář |
| Masaryk University / CESNET (MUNI) | WP4 — Federated computing; leads: Vojtěch Bystrý, Lukáš Hejtmánek |
| UCT Prague (VŠCHT) | WP5 — Training; lead: Vojtěch Spiwok |
| University of South Bohemia (ČBU/JČU) | WP5 — Training; lead: Rudolf Vohnout |
GET INVOLVED
Follow the Project
Are you a researcher working in life sciences, AI or data management? ELIXIR IMPACT training events are open to the research community. Follow our progress and be among the first to access new tools, datasets and training materials.
Website: www.elixir-czech.cz · Contact: elixir@uochb.cas.cz
ELIXIR IMPACT is funded by the Czech–Swiss Cooperation Programme (MŠMT ČR, call 8K2502), with 85 % Swiss contribution and 15 % Czech national co-funding. Project ID: 8K0205 · 2026–2028
