FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research
Scientific Data, vol. 9, pp. 169
Abstract
The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data and consent are captured in different ways and stored across many systems and organizations. This makes it difficult to discover rare disease patients, reuse data for personalized medicine and establish research cohorts based on specific parameters. FAIR Genomes aims to enable NGS data reuse by developing metadata standards for the data descriptions needed to FAIRify genomic data while also addressing ELSI issues. We developed a semantic schema of essential data elements harmonized with international FAIR initiatives. The FAIR Genomes schema v1.1 contains 110 elements in 9 modules. It reuses common ontologies such as NCIT, DUO and EDAM, only introducing new terms when necessary. The schema is represented by a YAML file that can be transformed into templates for data entry software (EDC) and programmatic interfaces (JSON, RDF) to ease genomic data sharing in research and healthcare. The schema, documentation and MOLGENIS reference implementation are available at https://fairgenomes.org .
Authors 23
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University Medical Center Groningen · University of Groningen
Affiliation as printed
University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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Radboud University Nijmegen · Radboud University Medical Center · Radboud Institute for Molecular Life Sciences
Affiliation as printed
Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
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Leiden University Medical Center
Affiliation as printed
Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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Radboud University Nijmegen · Radboud University Medical Center · Radboud Institute for Molecular Life Sciences
Affiliation as printed
Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
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Amsterdam UMC Location University of Amsterdam · Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Amsterdam University Medical Center, University of Amsterdam, Department of Pathology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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The Netherlands Cancer Institute
Affiliation as printed
The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
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Affiliation as printed
Prinses Máxima Center for Pediatric Oncology, Kemmeren group, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
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Radboud University Nijmegen · Radboud University Medical Center · Donders Institute for Brain, Cognition and Behaviour
Affiliation as printed
Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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University Medical Center Utrecht
Affiliation as printed
University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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Affiliation as printed
Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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Nationaal ICT Instituut in de Zorg
Affiliation as printed
Nictiz - Dutch competence centre for electronic exchange of health and care information, Oude Middenweg 55, 2491 AC, The Hague, The Netherlands
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Radboud University Nijmegen · Radboud University Medical Center
Affiliation as printed
Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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University Medical Center Utrecht
Affiliation as printed
University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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University Medical Center Utrecht
Affiliation as printed
University Medical Center Utrecht, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
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Affiliation as printed
Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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Radboud University Nijmegen · Radboud University Medical Center · Donders Institute for Brain, Cognition and Behaviour
Affiliation as printed
Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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Leiden University Medical Center · National Institute for Public Health and the Environment
Affiliation as printed
Leiden University Medical Center, Department of Clinical Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
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University Medical Center Groningen · University of Groningen
Affiliation as printed
University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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Vereniging Samenwerkende Ouder- en Patiëntenorganisaties
Affiliation as printed
VSOP - Patient Alliance for Rare and Genetic Diseases The Netherlands, Koninginnelaan 23, 3762 DA, Soest, The Netherlands
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Radboud University Nijmegen · Radboud University Medical Center · Radboud Institute for Molecular Life Sciences
Affiliation as printed
Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
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Vrije Universiteit Amsterdam · Amsterdam UMC Location Vrije Universiteit Amsterdam
Affiliation as printed
Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
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University Medical Center Groningen · University of Groningen
Affiliation as printed
University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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Morris A. Swertz corresponding
University Medical Center Groningen · University of Groningen
Affiliation as printed
University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. m.a.swertz@rug.nl
University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. m.a.swertz@rug.nl
University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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