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IHTSDO / snomed-owl-toolkit

The official SNOMED CT OWL Toolkit. OWL conversion, classification and authoring support.
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Clinical drug conversion (325875004) #74

Closed rwynne closed 1 year ago

rwynne commented 1 year ago

I am not certain if this is a content or conversion issue.

The following clinical drug in the December2022 Int'l release (http://snomed.info/id/325875004) does not have an EquivalentClasses axiom. Instead, the logical definition is on the subClassOf. The CD did not exist in the November2022 release.

with snomed-owl-toolkit version 3.0.9: > java -Xms4g -jar snomed-owl-toolkit-3.0.9-executable.jar -rf2-to-owl -rf2-snapshot-archives SnomedCT_InternationalRF2_PRODUCTION_20221231T120000Z.zip

image

rwynne commented 1 year ago

The SubClassOf relation is found in sct2_sRefset_OWLExpressionFull_INT_20221231.txt at line 24742.

$ grep -nP "\s325875004\s" sct2_sRefset_OWLExpressionFull_INT_20221231.txt
24742:8cb86bad-d940-42f2-8194-fe530287282c  20221231    1   900000000000207008  733073007   325875004   SubClassOf(:325875004 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:411116001 :385223009) ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:732943007 :395883003) ObjectSomeValuesFrom(:732945000 :258684004) ObjectSomeValuesFrom(:732947008 :732988008) ObjectSomeValuesFrom(:762949000 :395883003) DataHasValue(:1142135004 "12"^^xsd:decimal) DataHasValue(:1142136003 "1"^^xsd:decimal))) ObjectSomeValuesFrom(:763032000 :732988008) DataHasValue(:1142139005 "1"^^xsd:integer)))
129792:c2e72ee1-ab20-4d47-9d8f-6dacf3b9d6b8 20190731    1   900000000000207008  733073007   325875004   EquivalentClasses(:325875004 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:411116001 :385223009) ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:732943007 :395883003) ObjectSomeValuesFrom(:732944001 :82809009) ObjectSomeValuesFrom(:732945000 :258684004) ObjectSomeValuesFrom(:732946004 :38112003) ObjectSomeValuesFrom(:732947008 :732988008) ObjectSomeValuesFrom(:762949000 :395883003))) ObjectSomeValuesFrom(:763032000 :732988008) ObjectSomeValuesFrom(:766952006 :38112003)))
129793:c2e72ee1-ab20-4d47-9d8f-6dacf3b9d6b8 20210731    1   900000000000207008  733073007   325875004   EquivalentClasses(:325875004 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:411116001 :385223009) ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:732943007 :395883003) ObjectSomeValuesFrom(:732945000 :258684004) ObjectSomeValuesFrom(:732947008 :732988008) ObjectSomeValuesFrom(:762949000 :395883003) DataHasValue(:1142135004 "12"^^xsd:decimal) DataHasValue(:1142136003 "1"^^xsd:decimal))) ObjectSomeValuesFrom(:763032000 :732988008) DataHasValue(:1142139005 "1"^^xsd:integer)))
129794:c2e72ee1-ab20-4d47-9d8f-6dacf3b9d6b8 20211031    0   900000000000207008  733073007   325875004   SubClassOf(:325875004 ObjectIntersectionOf(:763158003 ObjectSomeValuesFrom(:411116001 :385223009) ObjectSomeValuesFrom(:609096000 ObjectIntersectionOf(ObjectSomeValuesFrom(:732943007 :395883003) ObjectSomeValuesFrom(:732945000 :258684004) ObjectSomeValuesFrom(:732947008 :732988008) ObjectSomeValuesFrom(:762949000 :395883003) DataHasValue(:1142135004 "12"^^xsd:decimal) DataHasValue(:1142136003 "1"^^xsd:decimal))) ObjectSomeValuesFrom(:763032000 :732988008) DataHasValue(:1142139005 "1"^^xsd:integer)))
kaicode commented 1 year ago

I can't answer this question but here is some background information..

A SubClassOf axiom has been used because the definition status of this concept has been set to "primitive" rather than "defined". This usually happens when the attributes in the axiom are not sufficient to define this type of concept.

This concept is very unusual. In the December International Release there are 22,318 descendants of 763760008 |Medicinal product categorized by structure (product)| and only two of them have a primitive definition status:

This is a content question. Please email info@snomed.org and the question will get routed to someone in the content team who has knowledge in this area.

pgwilliams commented 1 year ago

Agree, this concept has been defined as primitive, as we see in the SNOMED CT Browser (the empty yellow "pill" shape indicates a primitive definition status:

image

The "product" concept I'm not worried about because it's not been brought into line with the formal drug model, but the CD should - as I understood it - be sufficiently defined. I'll mention it to the terminologists here. Thanks for pointing this out @rwynne

rwynne commented 1 year ago

@pgwilliams This has always been my understanding, too. Thanks to you both!!

pgwilliams commented 1 year ago

@rwynne a terminologist got back to me to confirm that the concept should have been marked as sufficiently defined, and we'll get that fixed in the 2022-02-28 SNOMED CT International Edition release. Thanks again.

pgwilliams commented 1 year ago

This issue is not related to a fault with the snomed-owl-toolkit (it's purely a content problem); and in fact the toolkit is being quite faithful in its conversion, so I'll close this ticket.