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

التفاصيل البيبلوغرافية
العنوان: Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data.
المؤلفون: Kaliyaperumal R; Leiden University Medical Center, Leiden, The Netherlands., Wilkinson MD; 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., Moreno PA; 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., Benis N; Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands., Cornet R; Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands., Dos Santos Vieira B; Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands.; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands., Dumontier M; Institute of Data Science, Paul-Henri Spaaklaan 1, Maastricht University, 6229EN, Maastricht, The Netherlands., Bernabé CH; Leiden University Medical Center, Leiden, The Netherlands., Jacobsen A; Leiden University Medical Center, Leiden, The Netherlands., Le Cornec CMA; Division of Paediatric Nephrology, Centre for Paediatrics and Adolescent Medicine, University of Heidelberg, Heidelberg, Germany., Godoy MP; 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., Queralt-Rosinach N; Leiden University Medical Center, Leiden, The Netherlands., Schultze Kool LJ; Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands., Swertz MA; University of Groningen and University Medical Center Groningen, Genomics Coordination Center and Department of Genetics, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands., van Damme P; Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands., van der Velde KJ; University of Groningen and University Medical Center Groningen, Genomics Coordination Center and Department of Genetics, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands., Lalout N; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands.; Duchenne Parent Project, Veenendaal, The Netherlands., Zhang S; Department of Medical Informatics, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands., Roos M; Leiden University Medical Center, Leiden, The Netherlands.
المصدر: Journal of biomedical semantics [J Biomed Semantics] 2022 Mar 15; Vol. 13 (1), pp. 9. Date of Electronic Publication: 2022 Mar 15.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Biomed Central Country of Publication: England NLM ID: 101531992 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1480 (Electronic) NLM ISO Abbreviation: J Biomed Semantics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : Biomed Central
مواضيع طبية MeSH: Common Data Elements* , Rare Diseases*, Humans ; Registries ; Semantics ; Workflow
مستخلص: 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.
(© 2022. The Author(s).)
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فهرسة مساهمة: Keywords: Common data elements; Data transformation; Disease registries; FAIR data; Interoperability; Linked data; Ontologies; Rare disease; Semantic web
تواريخ الأحداث: Date Created: 20220316 Date Completed: 20220422 Latest Revision: 20220422
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8922780
DOI: 10.1186/s13326-022-00264-6
PMID: 35292119
قاعدة البيانات: MEDLINE
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