FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research.

Autor: van der Velde KJ; University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.; University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands., Singh G; Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands., Kaliyaperumal R; Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands., Liao X; Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands., de Ridder S; Amsterdam University Medical Center, University of Amsterdam, Department of Pathology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands., Rebers S; The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands., Kerstens HHD; Prinses Máxima Center for Pediatric Oncology, Kemmeren group, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands., de Andrade F; University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands., van Reeuwijk J; Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands., De Gruyter FE; University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands., Hiltemann S; Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands., Ligtvoet M; Nictiz - Dutch competence centre for electronic exchange of health and care information, Oude Middenweg 55, 2491 AC, The Hague, The Netherlands., Weiss MM; Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands., van Deutekom HWM; University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands., Jansen AML; University Medical Center Utrecht, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands., Stubbs AP; Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands., Vissers LELM; Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands., Laros JFJ; Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.; Leiden University Medical Center, Department of Clinical Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.; Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands., van Enckevort E; University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands., Stemkens D; VSOP - Patient Alliance for Rare and Genetic Diseases The Netherlands, Koninginnelaan 23, 3762 DA, Soest, The Netherlands., 't Hoen PAC; Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands., Beliën JAM; Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands., van Gijn ME; University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands., Swertz MA; 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. m.a.swertz@rug.nl.
Jazyk: angličtina
Zdroj: Scientific data [Sci Data] 2022 Apr 13; Vol. 9 (1), pp. 169. Date of Electronic Publication: 2022 Apr 13.
DOI: 10.1038/s41597-022-01265-x
Abstrakt: 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 .
(© 2022. The Author(s).)
Databáze: MEDLINE
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