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

K. Joeri van der Velde; Gurnoor Singh; Rajaram Kaliyaperumal; Xiao Feng 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

doi:10.1038/s41597-022-01265-x

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

K. Joeri van der Velde, Gurnoor Singh, Rajaram Kaliyaperumal, Xiao Feng 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. Beliën, Mariëlle E. van Gijn, Morris A. Swertz^*

^*Corresponding author for this work

Pathology

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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 language	English
Article number	169
Journal	Scientific data
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41597-022-01265-x
Publication status	Published - 13 Apr 2022

Bibliographical note

Acknowledgements:
We thank the FAIR Genomes Consortium, which is funded as a ZonMw “Personalized Medicine” project under award number 846003201. The FAIR Genomes Consortium members are listed in Supplementary Data S1. We acknowledge the following support for the authors: The FAIR genomes, under ZonMw Personalized Medicine program, No. 846003201 for K.J.V., G.S., X.L., S.R., J.R., S.H., M.M.W., A.P.S., L.E.M.L.V., J.F.J.L, E.E., D.S., P.A.C.H., J.A.M.B., M.E.G. and M.A.S. The European Union’s Horizon 2020 research and innovation program under the EJP RD COFUND-EJP No. 825575 for K.J.V., R.K., E.E., P.A.C.H. and M.A.S. The Netherlands X-Omics Initiative, partially funded by NWO, project no. 184.034.019 for K.J.V., G.S., X.L., P.A.C.H. and M.A.S. The WGS-first project, under ZonMW grant no. 843002608 and 846002003 for J.R., M.M.W and L.E.M.L.V. The Netherlands Organisation for Scientific Research NWO under VIDI grant number 917.164.455 for K.J.V. and M.A.S. The University Medical Center Utrecht for F.E.D.G., H.W.M.D. and A.M.L.J. Nictiz, Dutch competence centre for electronic exchange of health and care information for M.L. The EATRIS-Plus project funded through the Horizon 2020 – the European Union Framework Programme for Research and Innovation (Grant agreement ID: 871096) for P.A.C.H. The Dutch Cancer Society, grant number 11774 for S.d.R Grants from KiKa and Adessium Foundation for H.H.D.K. The University Medical Center Groningen for F.A. We thank the MOLGENIS team at UMCG Genomics Coordination Center for their help in developing and deploying the software, Erik Zwart for helping to test and document the import process of REDCap forms, and Fleur D.L. Kelpin and Max E. Postema for their help in creating the FAIR Genomes MOLGENIS Docker image. Finally, we would like to thank Kate McIntyre for editorial assistance.

Publisher Copyright: © 2022, The Author(s).

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van der Velde, K. J., Singh, G., Kaliyaperumal, R., Liao, X. F., de Ridder, S., Rebers, S., Kerstens, H. H. D., de Andrade, F., van Reeuwijk, J., De Gruyter, F. E., Hiltemann, S., Ligtvoet, M., Weiss, M. M., van Deutekom, H. W. M., Jansen, A. M. L., Stubbs, A. P., Vissers, L. E. L. M., Laros, J. F. J., van Enckevort, E., ... Swertz, M. A. (2022). FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. Scientific data, 9(1), Article 169. https://doi.org/10.1038/s41597-022-01265-x

@article{dd53453a53c542afad53bee58b15def5,

title = "FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research",

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.",

author = "{van der Velde}, {K. Joeri} and Gurnoor Singh and Rajaram Kaliyaperumal and Liao, {Xiao Feng} and {de Ridder}, Sander and Susanne Rebers and Kerstens, {Hindrik H.D.} and {de Andrade}, Fernanda and {van Reeuwijk}, Jeroen and {De Gruyter}, {Fini E.} and Saskia Hiltemann and Maarten Ligtvoet and Weiss, {Marjan M.} and {van Deutekom}, {Hanneke W.M.} and Jansen, {Anne M.L.} and Stubbs, {Andrew P.} and Vissers, {Lisenka E.L.M.} and Laros, {Jeroen F.J.} and {van Enckevort}, Esther and Daphne Stemkens and {{\textquoteleft}t Hoen}, {Peter A.C.} and Beli{\"e}n, {Jeroen A.M.} and {van Gijn}, {Mari{\"e}lle E.} and Swertz, {Morris A.}",

note = "Acknowledgements: We thank the FAIR Genomes Consortium, which is funded as a ZonMw “Personalized Medicine” project under award number 846003201. The FAIR Genomes Consortium members are listed in Supplementary Data S1. We acknowledge the following support for the authors: The FAIR genomes, under ZonMw Personalized Medicine program, No. 846003201 for K.J.V., G.S., X.L., S.R., J.R., S.H., M.M.W., A.P.S., L.E.M.L.V., J.F.J.L, E.E., D.S., P.A.C.H., J.A.M.B., M.E.G. and M.A.S. The European Union{\textquoteright}s Horizon 2020 research and innovation program under the EJP RD COFUND-EJP No. 825575 for K.J.V., R.K., E.E., P.A.C.H. and M.A.S. The Netherlands X-Omics Initiative, partially funded by NWO, project no. 184.034.019 for K.J.V., G.S., X.L., P.A.C.H. and M.A.S. The WGS-first project, under ZonMW grant no. 843002608 and 846002003 for J.R., M.M.W and L.E.M.L.V. The Netherlands Organisation for Scientific Research NWO under VIDI grant number 917.164.455 for K.J.V. and M.A.S. The University Medical Center Utrecht for F.E.D.G., H.W.M.D. and A.M.L.J. Nictiz, Dutch competence centre for electronic exchange of health and care information for M.L. The EATRIS-Plus project funded through the Horizon 2020 – the European Union Framework Programme for Research and Innovation (Grant agreement ID: 871096) for P.A.C.H. The Dutch Cancer Society, grant number 11774 for S.d.R Grants from KiKa and Adessium Foundation for H.H.D.K. The University Medical Center Groningen for F.A. We thank the MOLGENIS team at UMCG Genomics Coordination Center for their help in developing and deploying the software, Erik Zwart for helping to test and document the import process of REDCap forms, and Fleur D.L. Kelpin and Max E. Postema for their help in creating the FAIR Genomes MOLGENIS Docker image. Finally, we would like to thank Kate McIntyre for editorial assistance. Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = apr,

day = "13",

doi = "10.1038/s41597-022-01265-x",

language = "English",

volume = "9",

journal = "Scientific data",

issn = "2052-4463",

publisher = "Nature Publishing Group",

number = "1",

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van der Velde, KJ, Singh, G, Kaliyaperumal, R, Liao, XF, de Ridder, S, Rebers, S, Kerstens, HHD, de Andrade, F, van Reeuwijk, J, De Gruyter, FE, Hiltemann, S, Ligtvoet, M, Weiss, MM, van Deutekom, HWM, Jansen, AML, Stubbs, AP, Vissers, LELM, Laros, JFJ, van Enckevort, E, Stemkens, D, ‘t Hoen, PAC, Beliën, JAM, van Gijn, ME & Swertz, MA 2022, 'FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research', Scientific data, vol. 9, no. 1, 169. https://doi.org/10.1038/s41597-022-01265-x

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 - Acknowledgements: We thank the FAIR Genomes Consortium, which is funded as a ZonMw “Personalized Medicine” project under award number 846003201. The FAIR Genomes Consortium members are listed in Supplementary Data S1. We acknowledge the following support for the authors: The FAIR genomes, under ZonMw Personalized Medicine program, No. 846003201 for K.J.V., G.S., X.L., S.R., J.R., S.H., M.M.W., A.P.S., L.E.M.L.V., J.F.J.L, E.E., D.S., P.A.C.H., J.A.M.B., M.E.G. and M.A.S. The European Union’s Horizon 2020 research and innovation program under the EJP RD COFUND-EJP No. 825575 for K.J.V., R.K., E.E., P.A.C.H. and M.A.S. The Netherlands X-Omics Initiative, partially funded by NWO, project no. 184.034.019 for K.J.V., G.S., X.L., P.A.C.H. and M.A.S. The WGS-first project, under ZonMW grant no. 843002608 and 846002003 for J.R., M.M.W and L.E.M.L.V. The Netherlands Organisation for Scientific Research NWO under VIDI grant number 917.164.455 for K.J.V. and M.A.S. The University Medical Center Utrecht for F.E.D.G., H.W.M.D. and A.M.L.J. Nictiz, Dutch competence centre for electronic exchange of health and care information for M.L. The EATRIS-Plus project funded through the Horizon 2020 – the European Union Framework Programme for Research and Innovation (Grant agreement ID: 871096) for P.A.C.H. The Dutch Cancer Society, grant number 11774 for S.d.R Grants from KiKa and Adessium Foundation for H.H.D.K. The University Medical Center Groningen for F.A. We thank the MOLGENIS team at UMCG Genomics Coordination Center for their help in developing and deploying the software, Erik Zwart for helping to test and document the import process of REDCap forms, and Fleur D.L. Kelpin and Max E. Postema for their help in creating the FAIR Genomes MOLGENIS Docker image. Finally, we would like to thank Kate McIntyre for editorial assistance. Publisher Copyright: © 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.

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

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