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

Autor:	Núria Queralt-Rosinach, M. Prieto Godoy, K. J. van der Velde, N. Benis, Mark Wilkinson, S. Zhang, R. Kaliyaperumal, N. van Lin, C. Henrique Bernabe, Annika Jacobsen, L.J. Schultze Kool, C. M. A. Le Cornec, Marco Roos, Michel Dumontier, B. dos Santos Vieira, P. Alarcon Moreno, Ronald Cornet, P. van Damme, Morris A. Swertz
Přispěvatelé:	RS: FSE DACS IDS, Institute of Data Science, RS: FSE BISS, RS: FSE Studio Europa Maastricht, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), APH - Methodology, Medical Informatics, APH - Global Health, Graduate School, APH - Quality of Care, APH - Digital Health
Jazyk:	angličtina
Rok vydání:	2022
Předmět:	Computer Networks and Communications Computer science Interoperability Vascular damage Radboud Institute for Health Sciences [Radboudumc 16] Health Informatics Disease registries Ontology (information science) Semantic data model Data transformation Workflow Data modeling World Wide Web Rare Diseases All institutes and research themes of the Radboud University Medical Center Description logic Human Phenotype Ontology Ontologies Humans Registries FAIR data Linked data Common data elements Semantics Computer Science Applications Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19] Rare disease Semantic web Information Systems
Zdroj:	Journal of biomedical semantics, 13(1):9. BioMed Central Ltd Journal of Biomedical Semantics, 13, 1 Journal of Biomedical Semantics, 13(1). BMC Journal of Biomedical Semantics, 13(1):9. BMC Journal of Biomedical Semantics, 13 Journal of Biomedical Semantics, 13(1):9. BioMed Central Ltd.
ISSN:	2041-1480
Popis:	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.
Databáze:	OpenAIRE
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