Linking international registries to FHIR and Phenopackets with RareLink: a scalable REDCap-based framework for rare disease data interoperability
Abstract
, an open-source framework implementing our previously-published ontology-based rare disease common data model, enabling standardised data exchange between REDCap, international registries, and downstream analysis tools. Its preconfigured pipelines interact with the local REDCap application programming interface and enable semi-automatic import or export of data to the Global Alliance for Genomics and Health (GA4GH) Phenopackets and Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) instances, conforming to the HL7 International Patient Summary and Genomics Reporting profiles. The framework was developed in three iterative phases using retrospective and prospective clinical data from patients with various rare metabolic and neuromuscular disorders, as well as inborn errors of immunity. Phase one involved deployment across four German university hospitals for registry and data analysis purposes. Phase two integrated RareLink with the Canadian Inborn Errors of Immunity National Registry, enhancing extensibility. Phase three focuses on international implementation in South Africa and Japan to assess global scalability. Implementation feedback was continuously incorporated to validate outputs and improve usability. For evaluation purposes, we defined a simulated Kabuki syndrome cohort based on published cases and demonstrated data export to both Phenopackets and FHIR instances. RareLink can enhance the clinical utility of REDCap by enabling structured data analysis and interoperability. Its global applicability and open-source nature can support equitable rare disease research with the ultimate goal to improve patient care. Broader adoption and coordination with entities such as HL7 and the European Reference Networks are thus essential to realise its full potential. The framework and its documentation are freely available through GitHub and Read the Docs, respectively.
Authors 28
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University Hospital Cologne · Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
Institute for Biomedical Informatics, University Hospital Cologne, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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University of Cologne · University Hospital Cologne
Affiliation as printed
Medical Data Integration Center (MeDIC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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University of Cologne · University Hospital Cologne
Affiliation as printed
Medical Data Integration Center (MeDIC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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Affiliation as printed
Center for Rare Diseases, Medical Faculty, RWTH Aachen University, Aachen, Germany
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University of Cologne · University Hospital Cologne
Affiliation as printed
5. Department of Pediatrics and Adolescent Medicine, Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
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Universitätsmedizin Göttingen · University of Göttingen
Affiliation as printed
Department of Neurology, University Medical Center Goettingen, Germany
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Affiliation as printed
Department of Medical Informatics, University Medical Center Goettingen, Germany
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University of Calgary · Alberta Children's Hospital
Affiliation as printed
Section of Hematology and Immunology, Alberta Children's Hospital
University of Calgary, Calgary, Canada
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University of Calgary · Alberta Children's Hospital
Affiliation as printed
Section of Hematology and Immunology, Alberta Children's Hospital
University of Calgary, Calgary, Canada
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Affiliation as printed
Department of Pediatrics, Division of Immunology, Dalhousie University, IWK Health, Halifax, NS, Canada
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University of Calgary · Alberta Children's Hospital
Affiliation as printed
Section of Hematology and Immunology, Alberta Children's Hospital
University of Calgary, Calgary, Canada
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Stellenbosch University · Tygerberg Hospital
Affiliation as printed
Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
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Affiliation as printed
Department of Informatics for Genomic Medicine, ToMMo, Tohoku University, Miyagi, Japan
INGEM, Tohoku University, Miyagi, Japan
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University of Cologne · University Hospital Cologne
Affiliation as printed
5. Department of Pediatrics and Adolescent Medicine, Faculty of Medicine and University Hospital Cologne University of Cologne Cologne Germany
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Charité - Universitätsmedizin Berlin
Affiliation as printed
Center for Chronically Sick Children, Charité Universitätsmedizin Berlin, Germany
Department of Pediatric Endocrinology and Diabetology, Charité University Hospital, Berlin, Germany
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Charité - Universitätsmedizin Berlin · Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Center for Rare Diseases - Charité University Hospital, Berlin, Germany
Department of Pediatric Endocrinology and Diabetology, Charité University Hospital, Berlin, Germany
Deutsches Zentrum für Kinder- und Jugendgesundheit (DZKJ), partner site Berlin, Germany
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Lawrence Berkeley National Laboratory
Affiliation as printed
Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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University of North Carolina at Chapel Hill
Affiliation as printed
Department of Genetics, University of North Carolina Chapel Hill, USA
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin · The Jackson Laboratory for Genomic Medicine
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States
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Berlin Institute of Health at Charité - Universitätsmedizin Berlin
Affiliation as printed
Berlin Institute of Health at Charité Universitätsmedizin Berlin, Germany
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Affiliation as printed
Institute for Biomedical Informatics, University Hospital Cologne, Germany
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