Reasoning

• Capture truths in domain logic.
• Leverage that to ask general questions.
• - - -
• Avoid false-dichotomies around granularity.
• Get the computer to do stupid crap we don't want to do.

TermInfo Opportunity

TermInfo Opportunity

TermInfo Opportunity

TermInfo example

PREFIX sctid: <http://snomed.info/id/>
amy:Obs1 a fhir:Observation;
   fhir:code      [
      a fhir:CodeableConcept;
      fhir:coding ( [
         a           sctid:69896004;
         fhir:system [ fhir:v "http://snomed.info/sct" ];
         fhir:code   [ fhir:v "69896004" ]
      ] )
   ]
.

Start with a rich predicate ontology

fhir:Patient a owl:Class ; rdfs:label "fhir patient" .
fhir:code a owl:ObjectProperty; rdfs:label "fhir:code" .
fhir:Codeablecoding a owl:ObjectProperty; rdfs:label "fhir:Codeablecoding" .
fhir:system a owl:ObjectProperty; rdfs:label "fhir:system" .
fhir:code a owl:ObjectProperty; rdfs:label "fhir:code" .
fhir:v a owl:DatatypeProperty; rdfs:label "fhir value" .

look for the code

fhir:code some (
  fhir:Codeablecoding some (
    fhir:code some (fhir:value value "69896004") ) )

fhir:Observation-of-Rheumatoid_arthritis-disorder a owl:Class ;
    rdfs:label "fhir Observation of Rheumatoidarthritis (disorder)" ;
    owl:equivalentClass [
        owl:onProperty fhir:code ;
        owl:someValuesFrom [
            owl:onProperty fhir:Codeablecoding ;
            owl:someValuesFrom [
                owl:onProperty fhir:code ;
                owl:someValuesFrom [
                    owl:onProperty fhir:v ;
                    owl:hasValue "69896004"
                ]
            ]
        ]
    ]
.

Data:

PREFIX sctid: <http://snomed.info/id/>
amy:Obs1 a fhir:Observation;
   fhir:code      [
      a fhir:CodeableConcept;
      fhir:coding ( [
         a           sctid:69896004;
         fhir:system [ fhir:v "http://snomed.info/sct" ];
         fhir:code   [ fhir:v "69896004" ]
      ] )
   ]
.

what about the system?

 fhir:Observation.code some (
   fhir:CodeableConcept.coding some (
     fhir:Coding.system some (fhir:v value "http://snomed.info/sct")
     and fhir:Coding.code some (fhir:v value "69896004") ) )

fhir:Observation-of-Rheumatoid_arthritis-disorder a owl:Class ;
    rdfs:label "fhir Observation of Rheumatoidarthritis (disorder)" ;
    owl:equivalentClass [
        owl:onProperty fhir:Observation.code ;
        owl:someValuesFrom [
            owl:onProperty fhir:CodeableConcept.coding ;
            owl:someValuesFrom [ owl:intersectionOf (
              [ owl:onProperty fhir:Coding.code ;
                owl:someValuesFrom
                  [ owl:onProperty fhir:v ;
                    owl:hasValue "69896004" ] ]
              [ owl:onProperty fhir:Coding.system ;
                owl:someValuesFrom
                  [ owl:onProperty fhir:v ;
                    owl:hasValue "http://snomed.info/sct"
                ] ]
            ) ]
        ]
    ]
.

can't reason about literals

[ owl:intersectionOf (
  [ owl:onProperty fhir:code ;
    owl:someValuesFrom
      [ owl:onProperty fhir:v ;
        owl:hasValue "69896004" ] ]
  [ owl:onProperty fhir:system ;
    owl:someValuesFrom
      [ owl:onProperty fhir:v ;
        owl:hasValue "http://snomed.info/sct"
    ] ]
) ] rdfs:subClassOf fhir:Codinng-of-Rheumatoid_arthritis-disorder .

later fixed with fhir:concept links

now we can look for Observations with that coding

 fhir:Observation.code some (
   fhir:CodeableConcept.coding some fhir:Codinng-of-Rheumatoid_arthritis-disorder )
    

fhir:Observation-of-Rheumatoid_arthritis-disorder a owl:Class ;
    rdfs:label "fhir Observation of Rheumatoidarthritis (disorder)" ;
    owl:equivalentClass [
        owl:onProperty fhir:Observation.code ;
        owl:someValuesFrom [
            owl:onProperty fhir:CodeableConcept.coding ;
            owl:someValuesFrom snomedct:Rheumatoid_arthritis-disorder
        ]
    ]
.

snomed subsumptions, either directly

 fhir:Observation.code some (
   fhir:CodeableConcept.coding some snomedct:Rheumatoid_arthritis-disorder )
    

fhir:Observation-of-Rheumatoid_arthritis-disorder a owl:Class ;
    rdfs:label "fhir Observation of Rheumatoidarthritis (disorder)" ;
    owl:equivalentClass [
        owl:onProperty fhir:Observation.code ;
        owl:someValuesFrom [
            owl:onProperty fhir:CodeableConcept.coding ;
            owl:someValuesFrom snomedct:Rheumatoid_arthritis-disorder
        ]
    ]
.

or via a connecting property

fhir:Observation.code some (
  fhir:CodeableConcept.coding some (
    fhir:concept some snomedct:Rheumatoid_arthritis-disorder ) )
    

fhir:Observation-of-Rheumatoid_arthritis-disorder a owl:Class ;
    rdfs:label "fhir Observation of Rheumatoidarthritis (disorder)" ;
    owl:equivalentClass [
        owl:onProperty fhir:Observation.code ;
        owl:someValuesFrom [
            owl:onProperty fhir:CodeableConcept.coding ;
            owl:someValuesFrom [
                owl:onProperty fhir:concept ;
                owl:someValuesFrom snomedct:Rheumatoid_arthritis-disorder
            ]
        ]
    ]
.

connect FHIR coding to SNOMED concept

fhir:Codinng-of-Rheumatoid_arthritis-disorder rdfs:subClassOf
  [ owl:onProperty fhir:concept ;
    owl:someValuesFrom snomedct:Rheumatoid_arthritis-disorder ].
    

now use SNOMED's hierarchy

by direct subclass:

fhir:Observation.code some (
  fhir:CodeableConcept.coding some (
    fhir:concept some snomedct:Arthritis-disorder ) )
    

by class restriction:

fhir:Observation.code some (
  fhir:CodeableConcept.coding some (
    fhir:concept some (snomedct:Inflammatory_disorder-disorder
      and (snomedct:role_group-attr some 
         (snomedct:Associated_morphology-attr some snomedct:Inflammatory_morphology-morph
          and snomedct:Finding_site-attr some snomedct:Structure_of_musculoskeletal_system-body))
    )))

importing with fhir:concept

[ owl:intersectionOf (
  [ owl:onProperty fhir:code ;
    owl:someValuesFrom
      [ owl:onProperty fhir:v ;
        owl:hasValue "69896004" ] ]
  [ owl:onProperty fhir:system ;
    owl:someValuesFrom
      [ owl:onProperty fhir:v ;
        owl:hasValue "http://snomed.info/sct"
    ] ]
) ] rdfs:subClassOf fhir:Codinng-of-Rheumatoid_arthritis-disorder .

PREFIX sctid: <http://snomed.info/id/>
amy:Obs1 a fhir:Observation;
   fhir:code      [
      a fhir:CodeableConcept;
      fhir:coding ( [
         a           sctid:69896004;
         fhir:system [ fhir:v "http://snomed.info/sct" ];
         fhir:code   [ fhir:v "69896004" ]
      ] )
   ]
.

amy:Obs1
  fhir:Observation.code [
    fhir:concept snomedct:Rheumatoid_arthritis-disorder # <-?
    fhir:CodeableConcept.coding [
      fhir:concept snomedct:Rheumatoid_arthritis-disorder
    ]
  ] .

get rid of some junk

recognizers:

[ owl:intersectionOf (
  [ owl:onProperty fhir:code ;
    owl:someValuesFrom
      [ owl:onProperty fhir:v ;
        owl:hasValue "69896004" ] ]
  [ owl:onProperty fhir:system ;
    owl:someValuesFrom
      [ owl:onProperty fhir:v ;
        owl:hasValue "http://snomed.info/sct"
    ] ]
) ] rdfs:subClassOf fhir:Coding-of-Rheumatoid_arthritis-disorder .

connective tissue:

fhir:Coding-of-Rheumatoid_arthritis-disorder rdfs:subClassOf
  [ owl:onProperty fhir:concept ;
    owl:someValuesFrom snomedct:Rheumatoid_arthritis-disorder ].

Seronegative_rheumatoid_arthritis

Rheumatoid_arthritis