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FHIR® is the registered trademark of HL7 and is used with the permission of HL7. The Flame Design mark is the registered trademark of HL7 and is used with the permission of HL7.
Amsterdam, 15-17 November | @fhir_furore | #fhirdevdays17 | www.fhirdevdays.com
FHIR RDF in Action
Harold Solbrig, Mayo Clinic
About Me – Harold Solbrig
• Began in 1972 doing nuclear reactor safety software
• Began medical computing 1975-78 – Berkeley Scientific Labs
• First commercial Unix sysop
• Hardware - disc controllers / television newsrooms
• Worked on ASN.1, ISO 11179 (X3/L8) (metadata), ISO TC 215 (healthcare), OMG, HL7, WHO, IHTSDO / SNOMED International, ISO TC 37 (terminology)
• BS in Maths and Computer Science, MsC in Software Engineering
• With Mayo Clinic 1999-today (more or less)
About Me – Harold Solbrig
FHIR RDF in Action - Outline
• FHIR RDF with SNOMED and OWL
• FHIR RDF and i2b2
• fhir.schema.org (if time allows)
FHIR Resource Instance in RDF
http://www.hl7.org/fhir/diagnosticreport-example-f201-brainct.ttl
RDF Turtle Syntax
RDF Rendering Extensions – Concept URIs
<http://snomed.info/id/394914008>JSON
RDF Rendering Extensions – Resource Types
Construct the actual URI
Resource Type
Ontology Header
Requirement: import FHIR URI Catalog• No ‘import in RDF’ – have to use OWL• owl:imports requires owl:Ontology• ‘f201.ttl’ vs. ‘f201’ – reasoners don’t
cope well with something that is botha fhir:DiagnosticReport and an owl:Ontology (ontology describesreport, not IS the report)
Stay tuned:• Looking at
http://hl7.org/fhir/owl/DiagnosticReport/f201 (or variant thereof) as an alternative
Using FHIR RDF with a DL reasoner
FHIR DiagnosticReportInstance
Reasoner
Class CancerDiagnosis == any DiagnosticReport w/ a dx of a type of malignant neoplasm
Instance is (or is not) an instance of Class CancerDiagnosis
Using FHIR RDF with a DL reasoner
Reasoner
ConclusionsClassification
Rules
Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
ClassificationRules
InstanceDescriptions
reference Definition of the classes and predicates used in a FHIR
Resource Instance
DomainKnowledge
reference
reference
FHIR Resource Instance
http://www.hl7.org/fhir/diagnosticreport-example-f201-brainct.ttl
Instance Descriptions – the FHIR URI Catalog
Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
ClassificationRules
fhir.ttlreference Definition of the classes and predicates used in a FHIR
Resource Instance
DomainKnowledge
reference
reference
Concept References – SNOMED CT
http://snomed.info/id/188340000
Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
ClassificationRules
fhir.ttlreference Definition of the classes and predicates used in a FHIR
Resource Instance
reference
reference
Classification Rule
Classification Rules
Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
Cancerreport.owl
fhir.ttlreference Definition of the classes and predicates used in a FHIR
Resource Instance
reference
reference
Loading the classification rules
https://github.com/BD2KOnFHIR/BLENDINGFHIRandRDF/yosemite_talk/cancerreport.owl
Run the Reasoner
Result
Restrict to Patients
Finalized Reports Only
Finalized Reports Only
Approach is “brittle”:
• Code system hierarchy is replicated as flattened strings
• No link to fact that system is being used
• DataProperty constraints potentially make reasoner more complex
Finalize Reports Only – Proposed Solution
Finalized Reports Only (cont)
Finalized Patient Reports with Cancer Diagnosis
Result
Post-coordinated expressions
One possible format for compositional expression
Equivalent expression in OWL
https://github.com/BD2KOnFHIR/BLENDINGFHIRandRDF/yosemite_talk/diagnosticreport-example-thyroidtumor.ttl
363346000 - Malignant tumor363698006 – Finding Site170787008 – Left lobe of thyroid gland
Post coordinated classifier
…Declaration(Class(:ReportOfThyroidDisease))AnnotationAssertion(dc:title :ReportOfThyroidDisease
"Thyroid Disease Dx - disorder of the thyroid gland (sct:14304000)")EquivalentClasses(:ReportOfThyroidDisease ObjectSomeValuesFrom(fhir:DiagnosticReport.codedDiagnosis.coding sct:14304000))
)
https://github.com/BD2KOnFHIR/BLENDINGFHIRandRDF/yosemite_talk/thyroidreport.owl
Results
i2FHIRb2 – FHIR in i2b2
• I2b2 – Informatics for Integrating Biology and the Bedside
• Underlying model is “Star Schema”
https://www.i2b2.org/
I2B2 Observation Fact Table
Core table maps encounter_num(which uniquely determines patient_num) + (…) + concept_cd + modifier_cd a data type instance.
I2b2 Ontology Table
Ontology table maps a hierarchical path to…
… a SQL query that (amongst other things) …
… returns a set of concept codes + (optional) modifier codes
… that are used to select rows in the observation fact table
Loading FHIR into i2b2
FHIR Metadata Vocabulary
(fhir.ttl)I2B2 Ontology Cell
FHIR Resource Instance
FHIR Resource Instance1
FHIR Resource Instance1
FHIR Resource Instance
(RDF)
I2B2 CRC Cell(Observation_fact,
patient_dimension, etc.)
generate_i2b2
loadfacts
FHIR Resource Instance(JSON)
FHIR Resource Instance(JSON)
jsontordflibrary
https://github.com/BD2KOnFHIR/i2FHIRb2https://github.com/BD2KOnFHIR/jsontordf
i2b2 queries
I2B2 Ontology Cell
I2b2 Client
I2B2 CRC Cell(Observation_fact,
patient_dimension, etc.)
Navigation
Query
Matching Patients
fhir.ttl i2b2 ontology cell
FHIR Metadata Vocabulary Entry
I2B2 Ontology Table
I2b2 Ontology Navigation
FHIR Observation Resource I2B2 Ontology
I2b2 Observation Fact Table
FHIR in i2b2 - Status
We have proven that it can work
Still have to:
• Merge FHIR data types w/ i2b2 value types
• Add URIs (codes) for values themselves for queries
• Demonstrate that ontology can be re-structured to show clinical view rather than FHIR Resource view
• https://github.com/BD2KOnFHIR/i2FHIRb2
fhir.schema.org
Question: Is there a place for the FHIR URI catalog in the schema.orgspace?
Schema.org
• HTML Markup• Focus on online services and products• Used by Google, Bing, Yahoo! and others• Formats:
• Microdata• RDFa 1.1 Lite• JSON-LD
Embedded Microdata
Health-lifesci.schema.org
Embedded JSON-LD
Fhir.schema.org - Clinical research data?
Embedded RDF-A
fhir.schema.org – Potential Use Cases
• Provenance for FHIR Narrative Text
• HTML FHIR Interchange Format
• Markup for personal device measurements
• Mapping for HL& Continuity of Care (CCD) and other data formats
• Markup for blogs and other Personal Health Records (PHR)
• Linking Medical Knowledge / Data / Products
Embedded RDF-A
fhir.schema.org
NOTE:
Service is not currently active - it had been located on an appspotURL – will be re-established if interests
Original location:
http://fhir.fhir-schema-org.appspot.com
Credits
This work is supported in part by NIH grants U01 HG009450 and U01 CA18094.
This work was conducted using the Protégé resource, which is supported by grant GM10331601 from the National Institute of General Medical Sciences of the United States National Institutes of Health.
Eric Prud’hommeaux David Booth Dr. Guoqian JiangGrahame Grieve
The HCLS working group