Version 1
: Received: 5 December 2023 / Approved: 6 December 2023 / Online: 6 December 2023 (10:26:48 CET)
How to cite:
van der Horst, E.; Unni, D.; Kopmels, F.; Armida, J.; Touré, V.; Franke, W.; Crameri, K.; Cirillo, E.; Österle, S. Bridging Clinical and Genomic Knowledge: An Extension of the SPHN RDF Schema for Seamless Integration and FAIRification of Omics Data. Preprints2023, 2023120373. https://doi.org/10.20944/preprints202312.0373.v1
van der Horst, E.; Unni, D.; Kopmels, F.; Armida, J.; Touré, V.; Franke, W.; Crameri, K.; Cirillo, E.; Österle, S. Bridging Clinical and Genomic Knowledge: An Extension of the SPHN RDF Schema for Seamless Integration and FAIRification of Omics Data. Preprints 2023, 2023120373. https://doi.org/10.20944/preprints202312.0373.v1
van der Horst, E.; Unni, D.; Kopmels, F.; Armida, J.; Touré, V.; Franke, W.; Crameri, K.; Cirillo, E.; Österle, S. Bridging Clinical and Genomic Knowledge: An Extension of the SPHN RDF Schema for Seamless Integration and FAIRification of Omics Data. Preprints2023, 2023120373. https://doi.org/10.20944/preprints202312.0373.v1
APA Style
van der Horst, E., Unni, D., Kopmels, F., Armida, J., Touré, V., Franke, W., Crameri, K., Cirillo, E., & Österle, S. (2023). Bridging Clinical and Genomic Knowledge: An Extension of the SPHN RDF Schema for Seamless Integration and FAIRification of Omics Data. Preprints. https://doi.org/10.20944/preprints202312.0373.v1
Chicago/Turabian Style
van der Horst, E., Elisa Cirillo and Sabine Österle. 2023 "Bridging Clinical and Genomic Knowledge: An Extension of the SPHN RDF Schema for Seamless Integration and FAIRification of Omics Data" Preprints. https://doi.org/10.20944/preprints202312.0373.v1
Abstract
The Swiss Personalized Health Network (SPHN) is a Swiss research infrastructure initiative that aims to facilitate the exchange of health-related data in a FAIR manner. The SPHN Dataset and SPHN RDF Schema form an essential part of the SPHN Semantic Interoperability Framework, which currently covers mostly clinical routine data. To facilitate the integration of omics data produced by the SPHN National Data Streams, a genomics extension was developed. This was done in close collaboration with clinicians, researchers, bioinformaticians, and data managers, from Swiss university hospitals, academic research groups and the omics platforms. Here, we present the genomics extension of the SPHN RDF Schema, which can be used to semantically describe genomics experiments and covers both clinical and research domains. The schema centers around the general omics process flow, with concepts that denote the individual steps, such as sample processing, assay, and data processing. Genomics-specific specializations are provided, such as library preparation, sequencing assay, and sequencing analysis. The schema also facilitates in capturing other important omics metadata, such as information about the sequencing instrument, standard operating procedure, and quality control metrics. The extension aligns with existing semantic data models and reuses common biomedical vocabularies, such as EDAM, OBI and FAIR genomes, as value sets, thereby facilitating semantic interoperability. It will be used to FAIRify data that is produced within the Swiss network and to facilitate sharing this data as one knowledge graph for reuse among its participants.
Keywords
Genomics; FAIR; SPHN; RDF; NGS; clinical; data model; Semantic web
Subject
Medicine and Pharmacology, Other
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
