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IHTSDO / snomed-owl-toolkit

The official SNOMED CT OWL Toolkit. OWL conversion, classification and authoring support.
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Different hierachy in Protege and the SNOMED CT Browser #93

Closed rombaum closed 3 months ago

rombaum commented 3 months ago

I have the issue that I see a difference hierarchy for multiple concept from SNOMED CT in Protege and in the SNOMED CT Browser. I will describe the issue and my workflow with the following example:

I use the following command

java --add-opens java.base/java.lang=ALL-UNNAMED -Xms4g -jar snomed-owl-toolkit-5.4.0-executable.jar -rf2-to-owl -rf2-snapshot-archives SnomedCT_InternationalRF2.zip

to create the owl file from the Snomed RF2 files (version 2024-06-01). When I have a look into the SNOMED CT Browser (version 2024-06-01) for 1,1-Dichloro-2,2-bis(p-chlorophenyl)ethane measurement (procedure) I have 4 parents before reaching the concept Procedure (procedure).

1,1-Dichloro-2,2-bis(p-chlorophenyl)ethane measurement (procedure) in SNOMED CT Browser

When I open the generated owl file in Protege I have the following hierarchy:

1,1-Dichloro-2,2-bis(p-chlorophenyl)ethane measurement (procedure) in Protege

I also see that there is no direct relation between 1,1-Dichloro-2,2-bis(p-chlorophenyl)ethane measurement (procedure) and the respective parent defined (see on the right hand side under the property SubClass Of):

1,1-Dichloro-2,2-bis(p-chlorophenyl)ethane measurement (procedure) without parent class in Protege

Is there an issue in creating the hierarchy or is there a error in my workflow?

rwynne commented 3 months ago

@rombaum Is this an Asserted or Inferred view in Protege? To get a view like the SNOMED CT Browser you'll want the Inferred view of the hierarchy. Be sure the ELK Reasoner is installed as a plugin and is ran before toggling your view.

rombaum commented 3 months ago

@rombaum Is this an Asserted or Inferred view in Protege? To get a view like the SNOMED CT Browser you'll want the Inferred view of the hierarchy. Be sure the ELK Reasoner is installed as a plugin and is ran before toggling your view.

@rwynne thanks. Thats explains it all to me. Thanks!