Copia

[by Chimezie Ogbuji]

I just committed my working copy of the set of tools I use to manipulate and serialize SNOMED-CT (the Systematized Nomenclature of Medicine) and the Foundational Model of Anatomy (FMA) as OWL/RDF for use in the clinical terminology research I’ve been doing lately. It is still in a very rough form and probably not usable by anyone other than a Python / Semantic Web hacker such as myself. However, I’m hoping to get it to a shape where it can be used by others. I had hesitated to release it mostly because of my concerns around the SNOMED-CT license, but I’ve been assured that as long the hosting web site is based in the united states and (most importantly) the software is not released with the SNOMED distribution it should be okay.

I have a (mostly empty) Wiki describing the command-line invocation. It leverages InfixOWL and rdflib to manipulate the OWL/RDF. Basically, once you have loaded the delimited distribution into MySQL (the library also requires MySQLdb and an instance of MySQL to work with), you can run the command-line, giving it one or more list of SNOMED-CT terms (by their identifiers) and it will return an OWL/RDF representation of an extract from SNOMED-CT around those terms.

So, below is an example of running the command-line to extract a section around the term Diastolic Hypertension and piping the result to the FuXi commandline in order to select a single class (sno:HypertensiveDisorderSystemicArterial) and render it using (my preferred syntax for OWL: the Manchester OWL syntax):

$python ManageSNOMED-CT.py -e 48146000 -n short -s localhost -u ..mysql username.. --password=..mysql password.. -d snomed-ct | FuXi --ns=sno=tag:info@ihtsdo.org,2007-07-31:SNOMED-CT# --output=man-owl --class=sno:HypertensiveDisorderSystemicArterial --stdin
Class: sno:HypertensiveDisorderSystemicArterial
    ## Primitive Type (Hypertensive disorder) ##
    SNOMED-CT Code: 38341003 (a primitive concept)
    SubClassOf:
              Clinical finding
              Disease
              ( sno:findingSite some Systemic arterial structure )

Which renders an expression that can be paraphrased as

‘Hypertensive Disorder Systemic Arterial’ is a clinical finding and disease whose finding site is some structure of the systemic artery.

I can also take the Burn of skin example from the Wikipedia page on SNOMED and demonstrate the same thing, rendering it in its full (verbose) OWL/RDF/XML form:

<owl:Class rdf:about="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#BurnOfSkin">
  <owl:intersectionOf rdf:parseType="Collection">
    <owl:Restriction>
      <owl:onProperty>
        <owl:ObjectProperty rdf:about="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#findingSite"/>
      </owl:onProperty>
      <owl:someValuesFrom rdf:resource="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#SkinStructure"/>
    </owl:Restriction>
    <rdf:Description rdf:about="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#ClinicalFinding"/>
    <owl:Restriction>
      <owl:onProperty>
        <owl:ObjectProperty rdf:about="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#associatedMorphology"/>
      </owl:onProperty>
      <owl:someValuesFrom rdf:resource="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#BurnInjury"/>
    </owl:Restriction>
    <rdf:Description rdf:about="tag:info@ihtsdo.org,2007-07-31:SNOMED-CT#Disease"/>
  </owl:intersectionOf>
  <rdfs:label>Burn of skin</rdfs:label>
  <skos:scopeNote>disorder<skos:scopeNote>
  <skos:prefSymbol>284196006</skos:prefSmbol>
</owl:Class>

And then in its more palatable Manchester OWL form:

$ python ManageSNOMED-CT.py -e 284196006 -n short -s localhost -u ..username.. --password= -d snomed-ct | FuXi --ns=sno=tag:info@ihtsdo.org,2007-07-31:SNOMED-CT# --output=man-owl --class=sno:BurnOfSkin --stdin
Class: sno:BurnOfSkin
    ## A Defined Class (Burn of skin) ##
    SNOMED-CT Code: 284196006
    EquivalentTo:
      ( sno:ClinicalFinding and sno:Disease ) that
      ( sno:findingSite some Skin structure ) and (sno:associatedMorphology some Burn injury )

Which can be paraphrased as:

A clinical finding or disease whose finding site is some skin structure and whose associated morphology is injury via burn

The examples above use the ‘-n short’ option, which renders extracts in OWL via the short normal form which uses a procedure described in the SNOMED-CT manuals that produces a more canonical representation, eliminating redundancy in the process. It currently only works with the 2007-07-31 distribution of SNOMED-CT but I’m in the process of updating it to use the latest distribution. The latest distribution comes with its own OWL representation and I’m still trying to wrap my head around some quirks in it involving role groups and whether or not this library would need to change so it works directly off this OWL representation instead of the primary relational distribution format. Enjoy,