Harold Solbrig presented on representing FHIR resources as RDF and using description logic reasoning. Key points included: expressing a FHIR DiagnosticReport as RDF triples and OWL ontology, using an OWL reasoner to classify instances and derive new conclusions, and loading FHIR data into the i2b2 framework by converting to RDF. The talk also discussed post-coordinated expressions and potential uses of a fhir.schema.org vocabulary.

1. 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

2. 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)

3. About Me – Harold Solbrig

4. FHIR RDF in Action - Outline
• FHIR RDF with SNOMED and OWL
• FHIR RDF and i2b2
• fhir.schema.org (if time allows)

5. FHIR Resource Instance in RDF
http://www.hl7.org/fhir/diagnosticreport-example-f201-brainct.ttl

6. RDF Turtle Syntax

7. RDF Rendering Extensions – Concept URIs
<http://snomed.info/id/394914008>
JSON

8. RDF Rendering Extensions – Resource Types
Construct the actual URI
Resource Type

9. 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 both
a fhir:DiagnosticReport and an
owl:Ontology (ontology describes
report, not IS the report)
Stay tuned:
• Looking at
http://hl7.org/fhir/owl/DiagnosticRepor
t/f201 (or variant thereof) as an
alternative

10. Using FHIR RDF with a DL reasoner
FHIR DiagnosticReport
Instance
Reasoner
Class CancerDiagnosis == any DiagnosticReport w/ a dx of a
type of malignant neoplasm
Instance is (or is not) an
instance of Class
CancerDiagnosis

11. Using FHIR RDF with a DL reasoner
Reasoner
Conclusions
Classification
Rules

12. Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
Classification
Rules
Instance
Descriptions
reference Definition of the classes and
predicates used in a FHIR
Resource Instance
Domain
Knowledge
reference
reference

13. FHIR Resource Instance
http://www.hl7.org/fhir/diagnosticreport-example-f201-brainct.ttl

14. Instance Descriptions – the FHIR URI Catalog

15. Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
Classification
Rules
fhir.ttlreference Definition of the classes and
predicates used in a FHIR
Resource Instance
Domain
Knowledge
reference
reference

16. Concept References – SNOMED CT
http://snomed.info/id/188340000

17. Conclusions
Using FHIR RDF with a DL Reasoner
Reasoner
Classification
Rules
fhir.ttlreference Definition of the classes and
predicates used in a FHIR
Resource Instance
reference
reference

18. Classification Rule

19. Classification Rules

20. 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

21. Loading the classification rules
https://github.com/BD2KOnFHIR/BLENDINGFHIRandRDF/yosemite_talk/cancerreport.owl

22. Run the Reasoner

23. Result

24. Restrict to Patients

25. Finalized Reports Only

26. 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

27. Finalize Reports Only – Proposed Solution

28. Finalized Reports Only (cont)

29. Finalized Patient Reports with Cancer Diagnosis

30. Result

31. 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 tumor
363698006 – Finding Site
170787008 – Left lobe of thyroid gland

32. 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

33. Results

34. i2FHIRb2 – FHIR in i2b2
• I2b2 – Informatics for Integrating
Biology and the Bedside
• Underlying model is “Star Schema”
https://www.i2b2.org/

35. I2B2 Observation Fact Table
Core table maps encounter_num
(which uniquely determines
patient_num) + (…) + concept_cd +
modifier_cd  a data type instance.

36. 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

37. 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)
jsontordf
library
https://github.com/BD2KOnFHIR/i2FHIRb2
https://github.com/BD2KOnFHIR/jsontordf

38. i2b2 queries
I2B2 Ontology Cell
I2b2 Client
I2B2 CRC Cell
(Observation_fact,
patient_dimension, etc.)
Navigation
Query
Matching Patients

39. fhir.ttl  i2b2 ontology cell
FHIR Metadata Vocabulary Entry
I2B2 Ontology Table

40. I2b2 Ontology Navigation
FHIR Observation Resource I2B2 Ontology

41. I2b2 Observation Fact Table

43. 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

44. fhir.schema.org
Question: Is there a place for the
FHIR URI catalog in the schema.org
space?

45. 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

46. Embedded Microdata

47. Health-lifesci.schema.org

48. Embedded JSON-LD

49. Fhir.schema.org - Clinical research data?

50. Embedded RDF-A

51. 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

52. fhir.schema.org
NOTE:
Service is not currently active - it
had been located on an appspot
URL – will be re-established if
interests
Original location:
http://fhir.fhir-schema-org.appspot.com

53. 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 Jiang
Grahame Grieve
The HCLS working group