Research group description
 
Our laboratory has been a global reference in the development and implementation of the FAIR Data Principles (Findable, Accessible, Interoperable, and Reusable). We co-authored the original FAIR principles, designed the first objective, automatable metrics to measure FAIRness, and created software capable of autonomously evaluating and scoring digital objects. Today, our work focuses on FAIR-enabled federation, assessment, and innovative approaches to data modelling and interface design.

OSTrails – Open Science Plan, Track, Assess (Horizon Europe)
OSTrails fosters FAIR-oriented research by linking planning, monitoring, and evaluation. It transforms static Data Management Plans into machine-actionable, interoperable “living” documents (maDMPs), ensuring integration across the research lifecycle. Its Scientific Knowledge Graphs (SKGs) interconnect datasets, publications, and workflows, providing transparent evidence of FAIR adoption. The FAIR Evaluation enables machine-executable assessments with embedded guidance, making FAIR evaluation actionable and continuous.

ERDERA – European Rare Disease Research Alliance (Horizon Europe)
ERDERA strengthens the rare disease research ecosystem by enhancing collaboration among national and European infrastructures. Building on the EJP RD, it promotes translation of discoveries into medical interventions and the integration of FAIR data and advanced analytics. It provides training, technical support, and FAIR-enabling tools, fostering community engagement and equitable patient participation. Through coordinated governance and National Mirror Groups, ERDERA integrates researchers, clinicians, data stewards, and patients into a unified multi-stakeholder network.

FLAIR-GG – FAIRification, Linking and Integrated Reuse of Global ex situ Plant Germplasm Resources
FLAIR-GG addresses data fragmentation in plant germplasm collections. It establishes local FAIR Data Points in seedbanks for machine-readable metadata publication, a dynamic network index to interconnect them, and a virtual platform for federated search and data integration. An RDF transformation pipeline enables interoperability across heterogeneous sources, linking germplasm data with environmental and soil datasets. The project turns seedbanks into interconnected data centers supporting research, conservation, and European initiatives such as EURISCO.

European Joint Programme on Rare Diseases (EJP RD)
EJP RD created a federated ecosystem to connect rare disease resources (registries, biobanks, multi-omics repositories, and knowledge bases) under FAIR principles. Its Virtual Platform acts as a single access point, allowing federated discovery and query of distributed data while preserving privacy and respecting access conditions. By linking data sources through interoperable standards, EJP RD supports translational research, innovation, and regulatory science across the European rare disease landscape.

MULVIRISK – The Role of Multiple Infections in Plant Virus Infection Risk
MULVIRISK investigates how co-infections influence the emergence of new plant diseases in the context of global environmental change. Combining empirical and computational approaches, it analyzes pathogen interactions and develops simulation models to predict infection risks. The project also builds a FAIR-compliant database of plant-pathogen interactions, ensuring reusability and integration with broader agricultural data. It bridges ecology, bioinformatics, and FAIR data science to strengthen global food security.

Institutional FAIR Infrastructure
In collaboration with the CBGP Data Management and Administrative Teams, our group is building ontology-driven databases for managing institutional research data, improving interoperability and accessibility. A knowledge-based design allows all functionalities (data models and user interfaces) to be generated directly from an OWL ontology, enabling adaptable and FAIR-aligned information systems that unify personnel, projects, and publications.

 

Camara Ballesteros, Alberto - PhD Student

Curiel Manzanas, Sara - PhD Student

Wilkinson, Mark - Investigador senior programa Isaac Peral











  • 101156595. EUROPEAN RARE DISEASE RESEARCH ALLIANCE (ERDERA) 01/09/2024-31/08/2031.  European Union’s Horizon Europe research and innovation programme.

     

  • 101130187. OPEN SCIENCE PLAN TRACK ASSESS (OSTrails) 01/02/2024- 31/01/2027. European Union’s Horizon Europe framework programme.

     

  • PID2021-124671OB-I00. MULTIPLE INFECTIONS IN PLANT VIRUS RISK (MULVIRISK) 01/09/2023- 31/08/2025 (+ 6 months extension). Ministerio de Ciencia, Innovación/Agencia Estatal de Investigación (MCIN/AEI). PI: Fernando Garcia Arenal, Co-PI: Mark D Wilkinson

     

  • TED2021-130788B-I00. FAIRIFICATION, LINKING AND INTEGRATED REUSE OF GLOBAL EX SITU PLANT GERMOPLASM RESOURCES (FLAIR-GG). 1/12/2022 - 30/11/2024. Ministerio de Ciencia, Innovación/Agencia Estatal de Investigación (MCIN/AEI) and the EU NextGenerationEU/PRTR. PI: Mark D Wilkinson, Co-PI: Santiago Moreno

     

  • 825575. EUROPEAN JOINT PROGRAMME ON RARE DISEASES (EJP-RD). 01/02/2019-31/07/2024. European Union’s Horizon 2020 research and innovation programme.

     

  • BFU2017-82826-R. Clarification of the molecular mechanisms connecting the AMI1 knot with the balance between growth and defense. 01/01/2018, 30/09/2021.  PI:  Stephan Pollman, co-PI: Mark D Wilkinson

     

Lalout, N., Wilkinson, M.D., Wandrei, D., Tassoni, A., Atalaia, A., Prieto, M., Camara, A., Quemada, E., Franken, M., Jonker, A.H., Paliouras, G., Siminiuc, S., Carta, C., Dos Santos Vieira, B., Roos, M., Kaliyaperumal, R., Evangelista, T., ‘t Hoen, P.A.C., Vroom, E. 2026. The FAIR journey of a patient-driven registry: Reflections and practical solutions from the Duchenne Data Platform FAIRification experience. Journal of Neuromuscular Diseases 13, 304–315. DOI: 10.1177/22143602251382969

Lalout, N., Wilkinson, M.D., Wandrei, D., Tassoni, A., Atalaia, A., Prieto, M., Camara, A., Quemada, E., Franken, M., Jonker, A.H., Paliouras, G., Siminiuc, S., Carta, C., Dos Santos Vieira, B., Roos, M., Kaliyaperumal, R., Evangelista, T., ‘t Hoen, P.A.C., Vroom, E. 2025. The FAIR journey of a patient-driven registry: Reflections and practical solutions from the Duchenne Data Platform FAIRification experience. Journal of Neuromuscular Diseases 22143602251382970. DOI: 10.1177/22143602251382969

van Karnebeek, C.D.M., Müller, A.R., Benkemoun, L., Boussaad, I., Cornel, M.C., IntHout, J., de Kort, M., de Oliveira Martins, S., Prigione, A., Rigter, T., Roes, K.C.B., Sanchez, A., Schipper, R., Wilkinson, M.D., ’t Hoen, P.A.C. 2025. SIMPATHIC: Accelerating drug repurposing for rare diseases by exploiting SIMilarities in clinical and molecular PATHology. Molecular Genetics and Metabolism 144, 109073. DOI: 10.1016/j.ymgme.2025.109073

Cámara Ballesteros, A., Aguayo Jara, E., Verykaki, E.S., Pastor del Olmo, G., Moreno Vázquez, S., Torres, E., Wilkinson, M.D. 2024. The FLAIR-GG federated network of FAIR germplasm data resources. Scientific Data 11, 1386. DOI: 10.1038/s41597-024-04243-7

Hayn, D., Sandner, E., Vengadeswaran, A., Taru, E.-A., Wilkinson, M., Hanauer, M., Kreiner, K., Schreier, G. 2024. Privacy-Preserving Linkage of Distributed Pseudonymised Datasets in a Virtual European Rare Disease Platform. Digital Health and Informatics Innovations for Sustainable Health Care Systems 1442–1446. DOI: 10.3233/SHTI240683

Poza-Viejo, L., Payá-Milans, M., Wilkinson, M.D., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2024. Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time. Planta 260, 27. DOI: 10.1007/s00425-024-04454-7

Jeanson, F., Gibson, S.J., Alper, P., Bernier, A., Woolley, J.P., Mietchen, D., Strug, A., Becker, R., Kamerling, P., Sanchez Gonzalez, M. del C., Mah, N., Novakowski, A., Wilkinson, M.D., Benhamed, O.M., Landi, A., Krog, G.P., Müller, H., Riaz, U., Veal, C., Holub, P., van Enckevort, E., Brookes, A.J. 2024. Getting your DUCs in a row - standardising the representation of Digital Use Conditions. Scientific Data 11, 464. DOI: 10.1038/s41597-024-03280-6

Sanchez Gonzalez, M. del C., Kamerling, P., Iermito, M., Casati, S., Riaz, U., Veal, C.D., Maini, M., Jeanson, F., Benhamed, O.M., van Enckevort, E., Landi, A., Mimouni, Y., Le Cornec, C., Coviello, D.A., Franchin, T., Fusco, F., Ramírez García, J.A., van der Zanden, L.F.M., Bernier, A., Wilkinson, M.D., Mueller, H., Gibson, S.J., Brookes, A.J. 2024. Common conditions of use elements. Atomic concepts for consistent and effective information governance. Scientific Data 11, 465. DOI: 10.1038/s41597-024-03279-z

Wright, A., Wilkinson, M.D., Mungall, C., Cain, S., Richards, S., Sternberg, P., Provin, E., Jacobs, J.L., Geib, S., Raciti, D., Yook, K., Stein, L., Molik, D.C. 2024. FAIR Header Reference genome: a TRUSTworthy standard. Briefings in Bioinformatics 25, bbae122. DOI: 10.1093/bib/bbae122

Atalaia, A., Wandrei, D., Lalout, N., Thompson, R., Tassoni, A., ’t Hoen, P.A.C., Athanasiou, D., Baker, S.-A., Sakellariou, P., Paliouras, G., D’Angelo, C., Horvath, R., Mancuso, M., van der Beek, N., Kornblum, C., Kirschner, J., Pareyson, D., Bassez, G., Blacas, L., Jacoupy, M., Eng, C., Lamy, F., Plançon, J.-P., Haberlova, J., Brusse, E., Hoeijmakers, J.G.J., de Visser, M., Claeys, K.G., Paradas, C., Toscano, A., Silani, V., Gyenge, M., Reviers, E., Hamroun, D., Vroom, E., Wilkinson, M.D., Lochmuller, H., Evangelista, T. 2024. EURO-NMD registry: federated FAIR infrastructure, innovative technologies and concepts of a patient-centred registry for rare neuromuscular disorders. Orphanet Journal of Rare Diseases 19, 66. DOI: 10.1186/s13023-024-03059-3

Bernabé, C.H., Thielemans, L., Kaliyaperumal, R., Carta, C., Zhang, S., van Gelder, C.W.G., Benis, N., da Silva Santos, L.O.B., Cornet, R., Vieira, B. dos S., Lalout, N., Henriques, I., Ballesteros, A.C., Burger, K., Kersloot, M.G., Ehrhart, F., van Enckevort, E., Evelo, C.T., Gray, A.J.G., Hanauer, M., Hettne, K., de Ligt, J., Pereira, A., Queralt-Rosinach, N., Schultes, E., Taruscio, D., Waagmeester, A., Wilkinson, M.D., Willighagen, E.L., Jansen, M., Mons, B., Roos, M., Jacobsen, A. 2023. Building expertise on FAIR through evolving Bring Your Own Data (BYOD) workshops: describing the data, software, and management-focused approaches and their evolution. Data Intelligence 1–23. DOI: 10.1162/dint_a_00236

Alarcon, P., Braun, I., Hartley, E., Olson, D., Benis, N., Cornet, R., Wilkinson, M., Walls, R.L. 2023. Leveraging Biolink as a “Rosetta Stone” Between C-Path and EJP-RD Semantic Models Provides Emergent Interoperability. Journal of the Society for Clinical Data Management 2. DOI: 10.47912/jscdm.130

Mandakovic, D., Aguado-Norese, C., García-Jiménez, B., Hodar, C., Maldonado, J.E., Gaete, A., Latorre, M., Wilkinson, M.D., Gutiérrez, R.A., Cavieres, L.A., Medina, J., Cambiazo, V., Gonzalez, M. 2023. Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert. Environmental Microbiome 18, 24. DOI: 10.1186/s40793-023-00486-w

dos Santos Vieira, B., Bernabé, C.H., Zhang, S., Abaza, H., Benis, N., Cámara, A., Cornet, R., Le Cornec, C.M.A., ’t Hoen, P.A.C., Schaefer, F., van der Velde, K.J., Swertz, M.A., Wilkinson, M.D., Jacobsen, A., Roos, M. 2022. Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries. Orphanet Journal of Rare Diseases 17, 436. DOI: 10.1186/s13023-022-02558-5

Benhamed, O.M., Burger, K., Kaliyaperumal, R., da Silva Santos, L.O.B., Suchánek, M., Slifka, J., Wilkinson, M.D. 2022. The FAIR Data Point: Interfaces and Tooling. Data Intelligence 1–18. DOI: 10.1162/dint_a_00161

da Silva Santos, L.O.B., Burger, K., Kaliyaperumal, R., Wilkinson, M.D. 2022. FAIR Data Point: A FAIR-oriented approach for metadata publication. Data Intelligence 1–21. DOI: 10.1162/dint_a_00160

Ortiz-García, P., Pérez-Alonso, M.-M., González Ortega-Villaizán, A., Sánchez-Parra, B., Ludwig-Müller, J., Wilkinson, M.D., Pollmann, S. 2022. The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses. Frontiers in Plant Science 13. DOI: 10.3389/fpls.2022.928386

Kaliyaperumal, R., Wilkinson, M.D., Moreno, P.A., Benis, N., Cornet, R., dos Santos Vieira, B., Dumontier, M., Bernabé, C.H., Jacobsen, A., Le Cornec, C.M.A., Godoy, M.P., Queralt-Rosinach, N., Schultze Kool, L.J., Swertz, M.A., van Damme, P., van der Velde, K.J., Lalout, N., Zhang, S., Roos, M. 2022. Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data. Journal of Biomedical Semantics 13, 9. DOI: 10.1186/s13326-022-00264-6

Poza-Viejo, L., Payá-Milans, M., Martín-Uriz, P.S., Castro-Labrador, L., Lara-Astiaso, D., Wilkinson, M.D., Piñeiro, M., Jarillo, J.A., Crevillén, P. 2022. Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. Plant, Cell & Environment n/a. DOI: 10.1111/pce.14258

García-Jiménez, B., Muñoz, J., Cabello, S., Medina, J., Wilkinson, M.D. 2020. Predicting microbiomes through a deep latent space. Bioinformatics. DOI: 10.1093/bioinformatics/btaa971

Pérez-Alonso, M.-M., Ortiz-García, P., Moya-Cuevas, J., Lehmann, T., Sánchez-Parra, B., Björk, R.G., Karim, S., Amirjani, M.R., Aronsson, H., Wilkinson, M.D., Pollmann, S. 2020. Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and ABA, and trigger plant stress responses in Arabidopsis thaliana. Journal of Experimental Botany eraa485. DOI: 10.1093/jxb/eraa485

Prieto, M., Deus, H., Waard, A. de, Schultes, E., García-Jiménez, B., Wilkinson, M.D. 2020. Data-driven classification of the certainty of scholarly assertions. PeerJ 8, e8871. DOI: 10.7717/peerj.8871

Payá-Milans, M., Poza-Viejo, L., Martín-Uriz, P.S., Lara-Astiaso, D., Wilkinson, M.D., Crevillén, P. 2019. Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. GigaScience 8. DOI: 10.1093/gigascience/giz147

Wilkinson, M.D., Dumontier, M., Sansone, S.-A., Santos, L.O.B. da S., Prieto, M., Batista, D., McQuilton, P., Kuhn, T., Rocca-Serra, P., Crosas, M., Schultes, E. 2019. Evaluating FAIR maturity through a scalable, automated, community-governed framework. Scientific Data 6, 1–12. DOI: 10.1038/s41597-019-0184-5

García-Jiménez, B., Wilkinson, M.D. 2019. Robust and automatic definition of microbiome states. PeerJ 7, e6657. DOI: 10.7717/peerj.6657