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

被引：0

作者：

K. Joeri van der Velde

Gurnoor Singh

Rajaram Kaliyaperumal

XiaoFeng Liao

Sander de Ridder

Susanne Rebers

Hindrik H. D. Kerstens

Fernanda de Andrade

Jeroen van Reeuwijk

Fini E. De Gruyter

Saskia Hiltemann

Maarten Ligtvoet

Marjan M. Weiss

Hanneke W. M. van Deutekom

Anne M. L. Jansen

Andrew P. Stubbs

Lisenka E. L. M. Vissers

Jeroen F. J. Laros

Esther van Enckevort

Daphne Stemkens

Peter A. C. ‘t Hoen

Jeroen A. M. Beliën

Mariëlle E. van Gijn

Morris A. Swertz

机构：

[1] University of Groningen and University Medical Center Groningen,

[2] Genomics Coordination Center,undefined

[3] University of Groningen and University Medical Center Groningen,undefined

[4] Department of Genetics,undefined

[5] Radboud University Medical Center,undefined

[6] Radboud Institute for Molecular Life Sciences,undefined

[7] Center for Molecular and Biomolecular Informatics,undefined

[8] Leiden University Medical Center,undefined

[9] Department of Human Genetics,undefined

[10] Amsterdam University Medical Center,undefined

[11] University of Amsterdam,undefined

[12] Department of Pathology,undefined

[13] The Netherlands Cancer Institute,undefined

[14] Division of Molecular Pathology,undefined

[15] Prinses Máxima Center for Pediatric Oncology,undefined

[16] Kemmeren group,undefined

[17] Radboud University Medical Center,undefined

[18] Department of Human Genetics,undefined

[19] Donders Institute for Brain,undefined

[20] Cognition and Behaviour,undefined

[21] University Medical Center Utrecht,undefined

[22] Department of Genetics,undefined

[23] Erasmus Medical Center,undefined

[24] Department of Pathology,undefined

[25] Nictiz - Dutch competence centre for electronic exchange of health and care information,undefined

[26] Radboud University Medical Center,undefined

[27] Department of Human Genetics,undefined

[28] University Medical Center Utrecht,undefined

[29] Department of Pathology,undefined

[30] Leiden University Medical Center,undefined

[31] Department of Clinical Genetics,undefined

[32] Rijksinstituut voor Volksgezondheid en Milieu,undefined

[33] VSOP - Patient Alliance for Rare and Genetic Diseases The Netherlands,undefined

[34] Amsterdam University Medical Center,undefined

[35] Vrije Universiteit Amsterdam,undefined

[36] Department of Pathology,undefined

来源：

Scientific Data | / 9卷

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摘要：

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.

引用

共 30 条

[1] FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research
van der Velde, K. Joeri
Singh, Gurnoor
Kaliyaperumal, Rajaram
Liao, Xiaofeng
de Ridder, Sander
Rebers, Susanne
Kerstens, Hindrik H. D.
de Andrade, Fernanda
van Reeuwijk, Jeroen
De Gruyter, Fini E.
Hiltemann, Saskia
Ligtvoet, Maarten
Weiss, Marjan M.
van Deutekom, Hanneke W. M.
Jansen, Anne M. L.
Stubbs, Andrew P.
Vissers, Lisenka E. L. M.
Laros, Jeroen F. J.
van Enckevort, Esther
Stemkens, Daphne
Hoen, Peter A. C. t
Belien, Jeroen A. M.
van Gijn, Marielle E.
Swertz, Morris A.
SCIENTIFIC DATA, 2022, 9 (01)
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Hassanin, Emadeldin
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EUROPEAN JOURNAL OF HUMAN GENETICS, 2022, 30 (SUPPL 1) : 83 - 84
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RNA, 2018, 24 (10) : 1285 - 1296
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Chaitankar, Vijender
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Brooks, Matthew J.
Swaroop, Anand
PROGRESS IN RETINAL AND EYE RESEARCH, 2016, 55 : 1 - 31

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