Shape Expressions (ShEx) schemas for the FHIR R5 specification

Deepak K. Sharma; Eric Prud'hommeaux; David Booth; Claude Nanjo; Guoqian Jiang

doi:10.1016/j.jbi.2023.104534

Shape Expressions (ShEx) schemas for the FHIR R5 specification

Deepak K. Sharma, Eric Prud'hommeaux, David Booth, Claude Nanjo, Guoqian Jiang

Artificial Intelligence and Informatics

Research output: Contribution to journal › Article › peer-review

Abstract

This work continues along a visionary path of using Semantic Web standards such as RDF and ShEx to make healthcare data easier to integrate for research and leading-edge patient care. The work extends the ability to use ShEx schemas to validate FHIR RDF data, thereby enhancing the semantic web ecosystem for working with FHIR and non-FHIR data using the same ShEx validation framework. It updates FHIR's ShEx schemas to fix outstanding issues and reflect changes in the definition of FHIR RDF. In addition, it experiments with expressing FHIRPath constraints (which are not captured in the XML or JSON schemas) in ShEx schemas. These extended ShEx schemas were incorporated into the FHIR R5 specification and used to successfully validate FHIR R5 examples that are included with the FHIR specification, revealing several errors in the examples.

Original language	English (US)
Article number	104534
Journal	Journal of Biomedical Informatics
Volume	148
DOIs	https://doi.org/10.1016/j.jbi.2023.104534
State	Published - Dec 2023

Keywords

Clinical knowledge graphs
Data standards
Fast Healthcare Interoperability Resources (FHIR)
RDF graphs
Semantic web
Shape Expressions (ShEx)

ASJC Scopus subject areas

Health Informatics
Computer Science Applications

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10.1016/j.jbi.2023.104534

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title = "Shape Expressions (ShEx) schemas for the FHIR R5 specification",

abstract = "This work continues along a visionary path of using Semantic Web standards such as RDF and ShEx to make healthcare data easier to integrate for research and leading-edge patient care. The work extends the ability to use ShEx schemas to validate FHIR RDF data, thereby enhancing the semantic web ecosystem for working with FHIR and non-FHIR data using the same ShEx validation framework. It updates FHIR's ShEx schemas to fix outstanding issues and reflect changes in the definition of FHIR RDF. In addition, it experiments with expressing FHIRPath constraints (which are not captured in the XML or JSON schemas) in ShEx schemas. These extended ShEx schemas were incorporated into the FHIR R5 specification and used to successfully validate FHIR R5 examples that are included with the FHIR specification, revealing several errors in the examples.",

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AU - Booth, David

AU - Nanjo, Claude

AU - Jiang, Guoqian

PY - 2023/12

Y1 - 2023/12

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AB - This work continues along a visionary path of using Semantic Web standards such as RDF and ShEx to make healthcare data easier to integrate for research and leading-edge patient care. The work extends the ability to use ShEx schemas to validate FHIR RDF data, thereby enhancing the semantic web ecosystem for working with FHIR and non-FHIR data using the same ShEx validation framework. It updates FHIR's ShEx schemas to fix outstanding issues and reflect changes in the definition of FHIR RDF. In addition, it experiments with expressing FHIRPath constraints (which are not captured in the XML or JSON schemas) in ShEx schemas. These extended ShEx schemas were incorporated into the FHIR R5 specification and used to successfully validate FHIR R5 examples that are included with the FHIR specification, revealing several errors in the examples.

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Shape Expressions (ShEx) schemas for the FHIR R5 specification

Abstract

Keywords

ASJC Scopus subject areas

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