Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data

Journal of Biomedical Semantics, vol. 13, pp. 9

Abstract

BACKGROUND: The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles. RESULTS: Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR. CONCLUSIONS: Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.

Authors 19

1. Rajaram Kaliyaperumal Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

2. Mark D. Wilkinson corresponding

   Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria · Centre for Plant Biotechnology and Genomics · Universidad Politécnica de Madrid

   Affiliation as printed

   Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, ES, Spain. mark.wilkinson@upm.es

   Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, ES, Spain

3. Pablo Alarcón Moreno

   Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria · Centre for Plant Biotechnology and Genomics · Universidad Politécnica de Madrid

   Affiliation as printed

   Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, ES, Spain

4. Nirupama Benis

   Amsterdam Public Health · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands

5. Ronald Cornet

   Amsterdam Public Health · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands

6. Bruna dos Santos Vieira

   Radboud University Medical Center

   Affiliation as printed

   Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands

   Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands

7. Michel J. Dumontier

   Maastricht University

   Affiliation as printed

   Institute of Data Science, Paul-Henri Spaaklaan 1, Maastricht University, 6229EN, Maastricht, The Netherlands

8. César H. Bernabé Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

9. Annika Jacobsen Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center, Leiden, The Netherlands

10. Clémence M. A. Le Cornec

    Heidelberg University

    Affiliation as printed

    Division of Paediatric Nephrology, Centre for Paediatrics and Adolescent Medicine, University of Heidelberg, Heidelberg, Germany

11. Mario Prieto Godoy

    Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria · Centre for Plant Biotechnology and Genomics · Universidad Politécnica de Madrid

    Affiliation as printed

    Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón, Madrid, ES, Spain

12. Núria Queralt-Rosiñach Aachen

    Leiden University Medical Center

    Affiliation as printed

    Leiden University Medical Center, Leiden, The Netherlands

13. Leo J. Schultze Kool

    Radboud University Medical Center

    Affiliation as printed

    Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands

14. Morris A. Swertz

    University Medical Center Groningen · University of Groningen

    Affiliation as printed

    University of Groningen and University Medical Center Groningen, Genomics Coordination Center and Department of Genetics, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands

15. Philip van Damme

    Amsterdam Public Health · Amsterdam University Medical Centers · University of Amsterdam

    Affiliation as printed

    Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands

16. K. Joeri van der Velde

    University Medical Center Groningen · University of Groningen

    Affiliation as printed

    University of Groningen and University Medical Center Groningen, Genomics Coordination Center and Department of Genetics, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands

17. Nawel Lalout

    Radboud University Medical Center · Duchenne Parent Project

    Affiliation as printed

    Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands

    Duchenne Parent Project, Veenendaal, The Netherlands

18. Shuxin Zhang

    Amsterdam Public Health · Amsterdam University Medical Centers · University of Amsterdam

    Affiliation as printed

    Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands

19. Marco Roos Aachen

    Leiden University Medical Center

    Affiliation as printed

    Leiden University Medical Center, Leiden, The Netherlands