Swiss Personalized Health Network: Making health data FAIR in Switzerland
Creators: name: Unni, Deepak
name: Vasundra  Touré
name: Österle, Sabine
name: Crameri, Katrin
Publisher: name: F1000 Research Limited
Year: 2023

description: The Swiss Personalized Health Network (SPHN) is a national initiative under the leadership of the Swiss Academy of Medical Sciences (SAMS). In collaboration with the Swiss Institute of Bioinformatics SIB, the SPHN contributes to the development, implementation, and validation of coordinated data infrastructures in order to make clinical and health-related data available for research in Switzerland. Since future research questions and their data requirements are constantly evolving, the priority was to develop a purpose-independent description of existing data and knowledge rather than relying on existing data models which are typically focused on a specific use case.<br> <br> Together with partners at University Hospitals we have developed the SPHN Semantic Interoperability Framework that enables collaborative research by turning routine health data into FAIR1 (Findable, Accessible, Interoperable, Reusable) research data. The framework is built with a three pillar strategy that focuses on the definition of semantics for data unambiguity and standardization, data format specifications for data exchange, and explore use-cases and interoperability with external data models and initiatives. The framework also includes software tools and services to automate and facilitate the adoption of the semantics and data exchange.<br> <br> Concepts with defined semantics are specified in the so-called SPHN Dataset serving as a nationwide blueprint. The concepts function as reusable building blocks that can be combined to represent information. These concepts are linked to existing semantic standards (e.g. SNOMED CT, LOINC) and can be extended by projects to represent various data types of different medical disciplines. By adopting semantic web technologies - like Resource Description Framework (RDF), RDF Schema (RDFS), Web Ontology Language (OWL) - a specific SPHN RDF Schema3 has been built to encode the semantic concepts with given rules and conventions. To support the use of this schema and facilitate the work of stakeholders in using the SPHN Semantic Interoperability Framework, several other tools have been developed: <b>Dataset2RDF:</b> Tool that translates any SPHN-compliant Dataset to an SPHN-compliant RDF Schema <b>SPHN Schema Visualization Tool:</b> An extended implementation of pyLODE that generates an HTML document of a RDF schema <b>SHACLer:</b> Tool that automatically builds Shapes Constraint Language (SHACL) rules based on a given RDF schema for data validation purposes <b>SPARQLer:</b> Tool that automatically builds SPARQL Protocol and RDF Query Language (SPARQL) queries based on a given RDF schema for exploration of the data in triplestores <b>SPHN Schema Forge:</b> A web service that integrates the aforementioned tools to automate the generation of a RDF schema, SHACL rules, HTML visualization and SPARQL queries from an SPHN-compliant Dataset <b>DCC Terminology Service:</b> A service4 that generates machine-readable versions of national and international standards to facilitate their integration in a RDF schema To lower the entry barrier to this infrastructure, we provide training and documentation to facilitate knowledge sharing among all stakeholders. This framework is implemented in all Swiss university hospitals and forms the basis for future data-driven research projects with clinical and other health-related data. Work is currently underway to expand the framework also to other Swiss hospitals.<br> The SPHN Semantic Interoperability Framework and its tools are available on GitLab via https://git.dcc.sib.swiss/sphn-semantic-framework/. The documentation for the framework and its tools can be found at https://sphn-semantic-framework.readthedocs.io.