TY - JOUR
T1 - FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research
AU - van der Velde, K. Joeri
AU - Singh, Gurnoor
AU - Kaliyaperumal, Rajaram
AU - Liao, Xiao Feng
AU - de Ridder, Sander
AU - Rebers, Susanne
AU - Kerstens, Hindrik H.D.
AU - de Andrade, Fernanda
AU - van Reeuwijk, Jeroen
AU - De Gruyter, Fini E.
AU - Hiltemann, Saskia
AU - Ligtvoet, Maarten
AU - Weiss, Marjan M.
AU - van Deutekom, Hanneke W.M.
AU - Jansen, Anne M.L.
AU - Stubbs, Andrew P.
AU - Vissers, Lisenka E.L.M.
AU - Laros, Jeroen F.J.
AU - van Enckevort, Esther
AU - Stemkens, Daphne
AU - ‘t Hoen, Peter A.C.
AU - Beliën, Jeroen A.M.
AU - van Gijn, Mariëlle E.
AU - Swertz, Morris A.
N1 - © 2022. The Author(s).
PY - 2022/4/13
Y1 - 2022/4/13
N2 - 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.
AB - 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.
KW - Delivery of Health Care
KW - Genomics
KW - Humans
KW - Metadata
KW - High-Throughput Nucleotide Sequencing
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=85128148062&partnerID=8YFLogxK
U2 - 10.1038/s41597-022-01265-x
DO - 10.1038/s41597-022-01265-x
M3 - Article
C2 - 35418585
AN - SCOPUS:85128148062
SN - 2052-4463
VL - 9
SP - 169
JO - Scientific Data
JF - Scientific Data
IS - 1
M1 - 169
ER -