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Clinical data in FHIR
Intro & RDF representation
Josh Mandel, MD
SemanticWeb.com
December 12, 2014
What's the problem?
Healthcare workflows:
referrals and transitions of care
patient communications
quality improvement
clinical trial eligibility
→ need accessible data to flow
What is FHIR?
Draft standard within HL7
Open standard (→ CC0)
Resources, Datatypes, Value Sets ("80/20")
REST API
High conceptual alignment with sem web...
But vis-à-vis RDF, FHIR "reinvents" quite a bit.
What is FHIR? Resources
50+ "atomic" structures
What is FHIR? Datatypes
(Common structures for core meaning)
e.g. GET
All patients named "amy"
/Patient?name=amy
All combined systolic+diastolic measurements
/Observation?name:text=systolic+and+diastolic
/Observation?name=55284-4
/Observation?name=http://loinc.org|55284-4
What is FHIR? REST API
Chaining
"All blood pressures from females"
/Observation?name=55284-4&
subject:Patient.gender=F
Inclusion paths
"BP measurements with their component parts"
/Observation?name=55284-4&
_include=Observation.related.target
What is FHIR? REST API
What is FHIR? Profiles
("Meta" models used to describe resources)
Not required for individual patient data…
But a consistent way to host vocabs
Live demo
What is FHIR? ValueSet
80/20 principle for "core"
So everything is extensible (even primitives!)
"extension" vs. "modifierExtension"
"Note that, unlike in many other specifications, there can be no stigma
associated with the use of extensions by any application, project, or
standard - regardless of the institution or jurisdiction that uses or
defines the extensions. The use of extensions is what allows the FHIR
specification to retain a core simplicity for everyone."
What is FHIR? Extensibility
Data and reference material in one place
Rich query environment
Automated reasoning
● Clinical care
● Research
● Data quality analysis
FHIR in RDF. Why?
CodeableConcept → Coding
<name>
<coding>
<system value="http://loinc.org"/>
<code value="55284-4"/>
<display value="Blood pressure systolic and diastolic"/>
</coding>
</name>
FHIR in RDF. URIs
CodeableConcept → Coding
<name>
<text>BP</text>
<coding>
<system value="http://loinc.org"/>
<code value="55284-4"/>
<display value="Blood pressure systolic and diastolic"/>
</coding>
</name>
FHIR in RDF. URIs
http://loinc.org|55284-4
<birthDate value="1982-10-26"/>
Could express as
_:me fhirPatient:birthDate "1982-10-26".
FHIR in RDF. Dates, strings, etc.
<birthDate value="1982-10-26">
<extension url="http://myvocab/with-days">
<valueInteger="5"/>
</extension
</birthDate>
Explicit relations modeled… and extensible
FHIR in RDF. Relations
<Observation>
<subject value="Patient/123">
</Observation>
_:bp [
a fhir:Observation
Observation:subject [
a fhir:Reference;
Reference:reference <Patient/123>
]
].
Generate automated, simple transformations
Transparent syntactic manipulation
Verbose but comprehensive
FHIR in RDF. "Idiomatic RDF"?
→ Eventually we need
● idiomatic RDF
● readable ontology
● some automated reasoning

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Introduction-and-RDF-Representation-of-FHIR-for-Clinical-Data

  • 1. Clinical data in FHIR Intro & RDF representation Josh Mandel, MD SemanticWeb.com December 12, 2014
  • 2. What's the problem? Healthcare workflows: referrals and transitions of care patient communications quality improvement clinical trial eligibility → need accessible data to flow
  • 3. What is FHIR? Draft standard within HL7 Open standard (→ CC0) Resources, Datatypes, Value Sets ("80/20") REST API High conceptual alignment with sem web... But vis-à-vis RDF, FHIR "reinvents" quite a bit.
  • 4. What is FHIR? Resources 50+ "atomic" structures
  • 5. What is FHIR? Datatypes (Common structures for core meaning)
  • 6. e.g. GET All patients named "amy" /Patient?name=amy All combined systolic+diastolic measurements /Observation?name:text=systolic+and+diastolic /Observation?name=55284-4 /Observation?name=http://loinc.org|55284-4 What is FHIR? REST API
  • 7. Chaining "All blood pressures from females" /Observation?name=55284-4& subject:Patient.gender=F Inclusion paths "BP measurements with their component parts" /Observation?name=55284-4& _include=Observation.related.target What is FHIR? REST API
  • 8. What is FHIR? Profiles ("Meta" models used to describe resources)
  • 9. Not required for individual patient data… But a consistent way to host vocabs Live demo What is FHIR? ValueSet
  • 10. 80/20 principle for "core" So everything is extensible (even primitives!) "extension" vs. "modifierExtension" "Note that, unlike in many other specifications, there can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core simplicity for everyone." What is FHIR? Extensibility
  • 11. Data and reference material in one place Rich query environment Automated reasoning ● Clinical care ● Research ● Data quality analysis FHIR in RDF. Why?
  • 12. CodeableConcept → Coding <name> <coding> <system value="http://loinc.org"/> <code value="55284-4"/> <display value="Blood pressure systolic and diastolic"/> </coding> </name> FHIR in RDF. URIs
  • 13. CodeableConcept → Coding <name> <text>BP</text> <coding> <system value="http://loinc.org"/> <code value="55284-4"/> <display value="Blood pressure systolic and diastolic"/> </coding> </name> FHIR in RDF. URIs http://loinc.org|55284-4
  • 14. <birthDate value="1982-10-26"/> Could express as _:me fhirPatient:birthDate "1982-10-26". FHIR in RDF. Dates, strings, etc. <birthDate value="1982-10-26"> <extension url="http://myvocab/with-days"> <valueInteger="5"/> </extension </birthDate>
  • 15. Explicit relations modeled… and extensible FHIR in RDF. Relations <Observation> <subject value="Patient/123"> </Observation> _:bp [ a fhir:Observation Observation:subject [ a fhir:Reference; Reference:reference <Patient/123> ] ].
  • 16. Generate automated, simple transformations Transparent syntactic manipulation Verbose but comprehensive FHIR in RDF. "Idiomatic RDF"? → Eventually we need ● idiomatic RDF ● readable ontology ● some automated reasoning