owlcs / argo Goto Github PK

For example: Not declaring a custom annotation property is without a doubt a profile violation, while it certainly is most likely irrelevant to reasoning.

Almost all ontologies violate the fact that Version IRIs need to be absolute. Fixing it however causes another problem with the default repair strategy in the OWL API (which replaces the entire Ontology ID): If more than one ontologies in the imports closure have that problem, all will get the same ID. Which is again a (even more serious) violation.

@ignazio1977

I have run an analysis across all of Bioportal, this time the raw files instead of anything with imports merged. I found this picture insead (number is the number of ontologies affected):

useofundeclaredannotationproperty 201
useofundeclaredclass 85
illegalpunning 57
useofundeclaredobjectproperty 40
useofreservedvocabularyforclassiri 31
useofreservedvocabularyforannotationpropertyiri 23
insufficientindividuals 17
insufficientoperands 14
useofundeclareddatatype 12
useofundeclareddataproperty 12
useofnonsimplepropertyincardinalityrestriction 7
useofreservedvocabularyforobjectpropertyiri 6
useofnonsimplepropertyinasymmetricobjectpropertyaxiom 5
useofpropertyinchaincausescycle 3
lexicalnotinlexicalspace 3
useofnonsimplepropertyinirreflexivepropertyaxiom 2
datatypeirialsousedasclassiri 2
useofreservedvocabularyforontologyiri 1
useofnonsimplepropertyinfunctionalpropertyaxiom 1
useofnonsimplepropertyininversefunctionalobjectpropertyaxiom 1

Perhaps we should work off this list to agree on what repair to suggest.

Example given an otherwise empty ontology:
AnnotationAssertion(:A,hasSynonym,:B)
Should A and be have to be declared to pass the profile check?