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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