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Development of a FHIR RDF data transformation and validation framework and its evaluation

Eric Prud'Hommeaux, Josh Collins, David Booth, Kevin J. Peterson, Harold R. Solbrig,
Published: 1 May 2021
Journal of Biomedical Informatics , Volume 117; doi:10.1016/j.jbi.2021.103755

Abstract: Resource Description Framework (RDF) is one of the three standardized data formats in the HL7 Fast Healthcare Interoperability Resources (FHIR) specification and is being used by healthcare and research organizations to join FHIR and non-FHIR data. However, RDF previously had not been integrated into popular FHIR tooling packages, hindering the adoption of FHIR RDF in the semantic web and other communities. The objective of the study is to develop and evaluate a Java based FHIR RDF data transformation toolkit to facilitate the use and validation of FHIR RDF data. We extended the popular HAPI FHIR tooling to add RDF support, thus enabling FHIR data in XML or JSON to be transformed to or from RDF. We also developed an RDF Shape Expression (ShEx)-based validation framework to verify conformance of FHIR RDF data to the ShEx schemas provided in the FHIR specification for FHIR versions R4 and R5. The effectiveness of ShEx validation was demonstrated by testing it against 2693 FHIR R4 examples and 2197 FHIR R5 examples that are included in the FHIR specification. A total of 5 types of errors including missing properties, unknown element, missing resource Type, invalid attribute value, and unknown resource name in the R5 examples were revealed, demonstrating the value of the ShEx in the quality assurance of the evolving R5 development. This FHIR RDF data transformation and validation framework, based on HAPI and ShEx, is robust and ready for community use in adopting FHIR RDF, improving FHIR data quality, and evolving the FHIR specification.
Keywords: Fast Healthcare Interoperability Resources (FHIR) / Resource Description Framework (RDF) / Shape Expression (ShEx) / Semantic web / Data transformation / Quality assurance

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