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

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 StemkensPeter A. C. t Hoen, Jeroen A. M. Belien, Marielle E. van Gijn, Morris A. Swertz*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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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.

Original languageEnglish
Article number169
Number of pages13
JournalScientific data
Volume9
Issue number1
DOIs
Publication statusPublished - 13-Apr-2022

Keywords

  • NETWORK
  • WORKFLOW
  • CAPTURE
  • ATLAS

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