View source for HCLS/ClinicalObservationsInteroperability/Terminology/Ontologies

= representations of terminologies =

== Issues ==

=== Classes vs. Individuals ===

A given a hierarchy in some terminology:

  <span id="hierarchy" style="color:#a30">snomed:Infectious-disease-of-lung_disorder
    ⇧
  snomed:Infective-pneumonia_disorder
    ⇧
  snomed:Bacterial-pneumonia_disorder
    ⇧
  snomed:Secondary-bacterial-pneumonia_disorder</span>

can be expressed as a class hierarchy:

  <span id="valueset" style="color:#0a3">snomed:Infective-pneumonia_disorder rdfs:subClassOf snomed:Infectious-disease-of-lung_disorder .
  snomed:Bacterial-pneumonia_disorder rdfs:subClassOf snomed:Infective-pneumonia_disorder .
  snomed:Secondary-bacterial-pneumonia_disorder rdfs:subClassOf snomed:Bacterial-pneumonia_disorder .</span>

This is appropriate for use cases where the hierarchy is important, such as some CDS system which looks for more than one of the superclasses of '''snomed:Secondary-bacterial-pneumonia_disorder'''.
If that's not required, one can use a much more efficient closure to group terms into a single-level hierarchy.
For instance, if we simply want to collect all forms of infection lung diseases, we can represent the terms as a value set:

  <span id="valueset" style="color:#0a3">'''my''':Infectious-disease-of-lung_disorder snomed:Infective-pneumonia_disorder owl:oneOf (
  Infectious-disease-of-lung_disorder
  snomed:Bacterial-pneumonia_disorder
  snomed:Secondary-bacterial-pneumonia_disorder ).</span>

This is more efficient, at the expense of expressivity (the hierarchy is gone).
If we know the instance data will only use e.g. leaf-level codes, we can even eliminate the intermediate terns:

  <span id="valueset" style="color:#0a3">'''my''':Infectious-disease-of-lung_disorder owl:oneOf (
  snomed:Secondary-bacterial-pneumonia_disorder ). # plus viral + ...</span>


=== Concept Descriptor vs. IRI ===

Most clinical record systems use something like an ISO 21090 CD element with attributes to uniquely identifying a concept.

[[File:Example class ConceptDescriptor for-the ISO21090 Lynch 20101214.png|Description of Diagram of ISO 21090 Concept Descriptor (CD) Datatype (Detail)]]

The most critical these are the pair of '''codeSystem''' and '''code'''.
These effectively form a unique identier for a concept.
The concatonation of these can be viewed as a URN (like a URL, but not dereferencable).
Using the HL7 O-RIM Coding for 21090, the attributes look like:

  <span id="RFCD" style="color:#0a3">:labObs5678 <span style="color:#a30"># Joe's baseline measured in body fluid</span>
    a renal:RheumatoidFactorObservation ;
    hl7:coding [ <span style="background-color:#DFD">dt:CDCoding.code "13930-3" ; dt:CDCoding.codeSystem "2.16.840.1.113883.6.1" ;</span> <span style="color:#a30"># or EVS or ...</span>
                 <span style="background-color:#DFD"><span style="color:#777">dt:CDCoding.displayName 
    "Rheumatoid factor:Dilution Factor (Titer):Point in time:Synovial fluid (Joint fluid):Quantitative:Agglutination" ;
                 dt:CDCoding.codeSystemName "LOINC"</span></span> ] .</span>

Viewed as a URN, this could look like:

  <span id="RFURN" style="color:#0a3">:labObs5678 <span style="color:#a30"># Joe's baseline measured in body fluid</span>
    a renal:RheumatoidFactorObservation ;
    hl7:coding <urn:oidplus:2.16.840.1.113883.6.1/13930-3> .</span>

with some helpful metadata:

  <span id="RFaux" style="color:#0a3"><urn:oidplus:2.16.840.1.113883.6.1/13930-3>
    <span style="background-color:#DFD">dt:CDCoding.code "13930-3" ; dt:CDCoding.codeSystem "2.16.840.1.113883.6.1" ;</span> <span style="color:#a30"># or EVS or ...</span>
    <span style="background-color:#DFD"><span style="color:#777">dt:CDCoding.displayName 
    "Rheumatoid factor:Dilution Factor (Titer):Point in time:Synovial fluid (Joint fluid):Quantitative:Agglutination" ;
    dt:CDCoding.codeSystemName "LOINC"</span></span> .</span>

It is easy to use OWL equivalent class to assert the equivalence between these two forms:

  <span style="color:#03a" id="codeAndSystemToIRI"><urn:oidplus:2.16.840.1.113883.6.1/13930-3> 
    owl:equivalentClass [
      owl:intersectionOf (
        [ owl:onProperty dt:CDCoding.codeSystem ; owl:hasValue "2.16.840.1.113883.6.1" ]
        [ owl:onProperty dt:CDCoding.code       ; owl:hasValue "13930-3" ]
        ) ] .

== Resources ==
* [[HCLS/ClinicalObservationsInteroperability/FDATherapeuticAreaOntologies#Coding_specificity|example of LOINC as classes]]
* [http://webprotege.stanford.edu/#Edit:projectId=41dfe2d2-5096-4785-88cc-1ed09a0cfe0b alpha prototype of LOINC in OWL format.]
* [http://webprotege.stanford.edu/#Edit:projectId=41dfe2d2-5096-4785-88cc-1ed09a0cfe0b LOINC Ontology] (under development) captures axes.
* [http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=MTHU001879 Another LOINC Ontology] captures the complete set of LOINC codes.
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839278/ Semantic Web Representation of LOINC: an Ontological Perspective] pubmed/AMIA.
* [https://wiki.nci.nih.gov/display/SAIF/Domain+Analysis+Model+-+ISO+21090+Concept+Descriptor+%28CD%29+Datatype+%28Detail%29 NCI CD page]