SPARQL on FHIR

The FHIR specification defines RDF (specifically Turtle) as one of the possible serialization formats for FHIR resources. This means that every FHIR resource or a bundle of FHIR resources can be interpreted as an RDF dataset and queried using SPARQL.

I've created this tool to experiment with the RDF representation of FHIR resources and to demonstrate how FHIR data can be queried using SPARQL.

To use the tool, you need to provide the FHIR data in the FSH format and the SPARQL query.

FHIR resources (FSH instances)

Instance: obs1
InstanceOf: Observation
* identifier.use = #official
* identifier.system = "http://www.bmc.nl/zorgportal/identifiers/observations"
* identifier.value = "6323"
* status = #final
* code = http://loinc.org#15074-8 "Glucose [Moles/volume] in Blood"
* subject = Reference(Patient/pat1) "P. van de Heuvel"
* effectivePeriod.start = "2013-04-02T09:30:10+01:00"
* issued = "2013-04-03T15:30:10+01:00"
* performer = Reference(Practitioner/doc1) "A. Langeveld"
* valueQuantity = 6.3 'mmol/L' "mmol/l"
* interpretation = http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation#H "High"
* referenceRange.low = 3.1 'mmol/L' "mmol/l"
* referenceRange.high = 6.2 'mmol/L' "mmol/l"1
Instance: obs1
2
InstanceOf: Observation
3
* identifier.use = #official
4
* identifier.system = "http://www.bmc.nl/zorgportal/identifiers/observations"
5
* identifier.value = "6323"
6
* status = #final
7
* code = http://loinc.org#15074-8 "Glucose [Moles/volume] in Blood"
8
* subject = Reference(Patient/pat1) "P. van de Heuvel"
9
* effectivePeriod.start = "2013-04-02T09:30:10+01:00"
10
* issued = "2013-04-03T15:30:10+01:00"
11
* performer = Reference(Practitioner/doc1) "A. Langeveld"
12
* valueQuantity = 6.3 'mmol/L' "mmol/l"
13
* interpretation = http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation#H "High"
14
* referenceRange.low = 3.1 'mmol/L' "mmol/l"
15
* referenceRange.high = 6.2 'mmol/L' "mmol/l"

The FHIR resources (FSH instances) to be used for evaluating the SPARQL query.

SPARQL query

PREFIX fhir: <http://hl7.org/fhir/>

SELECT ?patient ?observationCode
WHERE {
  ?observation fhir:Observation.subject / fhir:link ?patient .
  ?observation fhir:Observation.code / fhir:CodeableConcept.coding / a ?observationCode .
}1
PREFIX fhir: <http://hl7.org/fhir/>
2

3
SELECT ?patient ?observationCode
4
WHERE {
5
  ?observation fhir:Observation.subject / fhir:link ?patient .
6
  ?observation fhir:Observation.code / fhir:CodeableConcept.coding / a ?observationCode .
7
}

The SPARQL query to be executed against the FHIR resources.

Output/Log

Press the Run query button to execute the query.

See also

FHIR resource models - Introduction to FHIR resource models + FHIR resource model browser.

FHIR resource graphs - Diving into FHIR resource graphs + FHIR graph viewer.

FHIR type tree - Visualizing the hierarchy of FHIR data types and resources.

FHIR Validator - What goes into checking if your FHIR resource conforms to the specification + online FHIR Validator.

FHIR Validation Client - Execute the $validate operation against a FHIR endpoint.

SMART on FHIR Testing Tool - Test SMART on FHIR app flows online.

FSH Compiler - Compile FHIR Shorthand code into FHIR JSON.

FSH Editor - Author and debug FSH documents online.

FHIRPath Testing Tool - Evaluate FHIRPath expressions against FHIR resources.

Awesome FHIRPath - A curated list of awesome resources on FHIRPath.

FHIRPath Client - Submit FHIRPath to FHIR servers for evaluation.

FHIRPath Editor - An online editor for FHIRPath expressions.

FHIR Mapping Language Compiler - Convert FHIR Mapping Language into StructureMap resources.

FHIR Mapping Language Testing Tool - Author and debug FHIR Mapping Language files.

HFQL Client - Query FHIR servers using HFQL online.

FHIR Converter - A converter for FHIR resources between different formats.

FHIR Viewer - Connect to and browse FHIR servers.

FHIR Quiz - Test your knowledge of the Fast Healthcare Interoperability Resources (FHIR) standard.

FHIR Structure Definition Snapshot Generator - Generate snapshots for FHIR StructureDefinitions.

FHIR Diff Tool (FHIR Diff Checker) - Compare two FHIR resources online.

FHIR GraphQL Client - Query FHIR stores using GraphQL.

FHIR Message Sender - Submit messages to FHIR servers.

List of national FHIR implementation guides - Implementation guides used by countries or specific regions.

What is FHIR and why is it important? - An overview of FHIR and its impact on patient care.

Awesome FHIR blogs - A curated list of awesome FHIR blogs.

FHIR icons - My set of vector icons for FHIR data elements.

Magic FHIR servers - Instant FHIR servers for testing and exploration, prepopulated with the FSH instances that are inlined in the server URLs.

FHIR Crossword - Test your knowledge of FHIR resources by solving a crossword puzzle.

CQL Testing Tool - Test CQL against FHIR resources.

CQL Editor - Edit CQL files online.

FHIR Measure Evaluator - Evaluate FHIR Measure resources online.

HL7v2-to-FHIR Converter - Convert HL7 messages to FHIR online.

Converting HL7v2 to FHIR - Translating HL7v2 messages to FHIR.

List of FHIR terminology servers - The list of FHIR-compliant servers for working with code systems, value sets, and concept maps.

FHIR Terminology Service Client - Query FHIR terminology services online.

CDS Hooks Testing Tool - Test CDS Hooks online.

Let's explore the Nobel Prize dataset - An overview of the official Nobel Prize Linked Data dataset with some example SPARQL queries.

How to query Wikidata using SPARQL in JavaScript - A guide to getting data from Wikidata using SPARQL in JavaScript.

SPARQL Parse Tree Viewer - Visualize the parse tree of SPARQL queries.

Introduction to SPARQL - SPARQL is a query language for graph data. The graph model of thinking fits well a lot of use cases.

Why federation is a game-changing feature of SPARQL - SPARQL federation is an incredibly useful feature for querying distributed RDF graphs.

SPARQL Client - Query SPARQL endpoints online.

SPARQL Playground (RDF Playground) - Experiment with running SPARQL queries against RDF data.

Magic SPARQL endpoints - Instant triplestores for testing and exploration, prepopulated with the RDF/Turtle data that is inlined in the SPARQL endpoint URLs.

List of public SPARQL endpoints - A list of public SPARQL endpoints for querying various RDF datasets.

SPARQL Editor - A simple online editor for SPARQL (SPARQL Protocol and RDF Query Language) queries.