Source files for Blending FHIR RDF and OWL

These files can be used to demonstrate the use of FHIR, RDF and SNOMED CT in the context of a Protege.

Instructions:

1. Clone this project
2. Download the latest version of Protégé Desktop
3. Copy catalog-remote.xml to catalog-v001.xml. This will retrieve the FHIR resources from the FHIR Build Server. (catalog-local.xml is an equivalent that retrives all resources locally).
4. Open wrapper.owl in Protégé
5. Select the Fact++ reasoner from the Reasoner tab
6. Select **Start Reasoner ** from the Reasoner tab
7. Switch to the Entities tab to see the results

The above image shows f201,a final diagnostic report of a '188340000 | Malignant tumor of craniopharyngeal duct', classified as an instance of FinalReportWithPatientCancerDiagnosis, prelimDX, a preliminary diagnostic report of the same thing classified as a ReportWithCancerDiagnosis and f201, a final diagnostic report of a '428763004 | Bacteremia due to staphylococcus|' classified as just a FinalizedReport.

Note that FinalizedReportWithCancerDiagnosis is a subclass of both FinalizedReport and ReportWithCancerDiagnosis, meaning that f201 is also an instance of both of those classifiers.

Files

OWL Files

• wrapper.owl: A wrapper ontology that imports all of the other ontologies needed for classification
• fhir.ttl: the FHIR ontology. Downloaded from: http://build.fhir.org/fhir.ttl
• w5.ttl: The FHIR "W5" (Who, What, Why, Where, When) Ontology. Downloaded from: http://build.fhir.org/w5.ttl
• snomed_subset.ttl: A small subset of SNOMED CT. Output of snomed_subset.sh
• rules.owl: Sample classification rules.
• diagnosticreport-example-f201-brainct.ttl: Example FHIR DiagnosticReport of a 188340000| Malignant tumor of craniopharyngeal duct |. Used to demonstrate ReportWithCancerDiagnosis classifier. Downloaded from: http://build.fhir.org/diagnosticreport-example-f201-brainct.ttl
• diagnosticreport-example-f201-prelim.ttl: Identical to f201-brainct.ttl with exception that report status was changed from 'final' to 'prelim'. Used to demonstrate FinalizedReport classifier.
• diagnosticreport-example-f202-bloodculture.ttl: Example FHIR DiagnosticReport of a |428763004| Bacteremia due to staphylococcus|. Example of a diagnostic report that is not about a 363346000| Malignant neoplastic disease |. Downloaded from: http://build.fhir.org/diagnosticreport-example-f202-bloodculture.ttl
• imagingstudy-example-xr.ttl: Example FHIR ImagingStudy with the SNOMED code 'T-15460' changed to '7467003|Wrist joint structure|' and '419161000|Unilateral left|' changed to '771000|Left|'. Used for demonstration / discussion of post-coordinated model classification. Source: http://build.fhir.org/imagingstudy-example-xr.ttl.
• medicationstatementexample1.ttl: Copy of http://build.fhir.org/medicationstatementexample1.ttl with the '''xsd:date''' types changed to '''xsd:dateTime''' because the FaCT++ reasoner chokes on straight dates. Used to demonstrate the FilmTabletMedication classifier.
• medicationstatementexample1bc.ttl: Copy of http://build.fhir.org/medicationstatementexample1bc.ttl with the '''xsd:date''' types changed to '''xsd:dateTime''' the dose from changed from '385057009|Film-coated tablet| to '42162004|buccal tablet|'.
• medicationstatementexample4.ttl: Copy of http://build.fhir.org/medicationstatementexample4.ttl with the '''xsd:date''' types changed to '''xsd:dateTime'''. Used to demonstrate the TabletDoseForm classifier.
• observation-example-bmd.ttl: Copy of http://build.fhir.org/observation-example-bmd.ttl with the post-coordinated SNOMED CT expression changed to its OWL equivalent.

Ancillary Files

• catalog-local.xml: An OASIS XML Catalog that only references local OWL files.
• catalog-remote.xml: An OASIS XML Catalog that references sources from the FHIR Build Server when they haven't been changed locally
• snomed_subset.json: configuration file used by the SNOMEDToOWL tool to generate the SNOMED CT subset.
• snomed_subset.sh: Shell script to generate snomed_subset.ttl

Building snomed_subset.ttl

1. Follow the installation instructions on the SNOMEDToOWL conversion page.
2. Download the latest image of SNOMED CT International. The US Download Site can be found at https://www.nlm.nih.gov/healthit/snomedct/index.html -- non US citizens need to consult SNOMED International for instructions on where to get SNOMED in their country.
3. Run RF2Filter to extract the desired subset. In the example below, we extract the RF2 for ancestors and descendants of '363346000 |Malignant neoplastic disease (disorder)|', '40238009 |Hand joint structure (body structure)|' and '385055001 |Tablet dose form (qualifier value)|' into the snomed_subset directory:

> RF2Filter -i -a -d SnomedCT_InternationalRF2_Production_20170131T120000/Snapshot snomed_subset 363346000 40238009 385055001

4. Run SNOMEDToOWL to generate OWL for the output RF2:

> SNOMEDToOWL snomed_subset snomed_subset.json snomed_subset.ttl