DL Profile violations

[pbuttigieg]

Detected in #1192, should we act on these? The QC checks pass, but there are many; how much of an issue can these be in applications?

Originally posted by @pbuttigieg in #1192 (comment)

From robot validate-profile --profile DL --input envo-edit.owl -vvv

OWL 2 DL Profile Report: Ontology and imports closure NOT in profile. The following violations are present:
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0019412> "envoPolar")]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0019332> "envoPolar")]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0019409> "envoPolar")]
Use of undeclared annotation property: <http://purl.org/dc/elements/1.1/title> in annotation [Annotation(<http://purl.org/dc/elements/1.1/title> "ENVO Bridge Axioms") in null]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000040> [SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_36342> <http://purl.obolibrary.org/obo/BFO_0000040>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIR
I(<null>))]
Use of undeclared annotation property: <http://purl.org/dc/elements/1.1/creator> in annotation [Annotation(<http://purl.org/dc/elements/1.1/creator> "http://orcid.org/0000-0002-6601-2165") in null]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000040> [SubClassOf(<http://purl.obolibrary.org/obo/CHEBI_24431> <http://purl.obolibrary.org/obo/BFO_0000040>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIR
I(<null>))]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0019331> "envoPolar")]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/PCO_0000002> "envoPolar")]
Use of undeclared object property: <http://purl.obolibrary.org/obo/RO_0002303> [SubClassOf(<http://purl.obolibrary.org/obo/PCO_0000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002303> <http://purl.obolibrary.org/obo/ENVO_01000739>)) in OntologyID(Ontolog
yIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<null>))]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0015948> "envoPolar")]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0015979> "envoPolar")]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0019414> "envoPolar")]
Use of undeclared class: <http://purl.obolibrary.org/obo/UBERON_0000061> [SubClassOf(<http://purl.obolibrary.org/obo/FAO_0000001> <http://purl.obolibrary.org/obo/UBERON_0000061>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) Ver
sionIRI(<null>))]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/GO_0019411> "envoPolar")]
Use of undeclared object property: <http://purl.obolibrary.org/obo/RO_0000056> [SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000002> Obj
ectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/ENVO_01001023>)))) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<null>))]
Use of undeclared annotation property: <http://purl.org/dc/terms/license> in annotation [Annotation(<http://purl.org/dc/terms/license> "https://creativecommons.org/publicdomain/zero/1.0/") in null]
Use of undeclared annotation property: <http://usefulinc.com/ns/doap#GitRepository> in annotation [Annotation(<http://usefulinc.com/ns/doap#GitRepository> "https://github.com/EnvironmentOntology/envo/"^^xsd:anyURI) in null]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000002> [SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000002> ObjectSomeVa
luesFrom(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/ENVO_01001023>)))) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<null>))]
Use of undeclared object property: <http://purl.obolibrary.org/obo/RO_0000052> [SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000002> Obj
ectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/ENVO_01001023>)))) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<null>))]
Use of undeclared class: <http://purl.obolibrary.org/obo/ENVO_01000739> [SubClassOf(<http://purl.obolibrary.org/obo/PCO_0000001> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002303> <http://purl.obolibrary.org/obo/ENVO_01000739>)) in OntologyID(OntologyIRI(<h
ttp://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<null>))]
Use of undeclared annotation property: <http://purl.org/dc/elements/1.1/description> in annotation [Annotation(<http://purl.org/dc/elements/1.1/description> "Bridge module that injects axioms connects external ontologies to upper ontology classes") in null]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000004> [SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0001062> <http://purl.obolibrary.org/obo/BFO_0000004>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) Versio
nIRI(<null>))]
Use of undeclared class: <http://purl.obolibrary.org/obo/ENVO_01001023> [SubClassOf(<http://purl.obolibrary.org/obo/PATO_0001739> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000002> ObjectSome
ValuesFrom(<http://purl.obolibrary.org/obo/RO_0000056> <http://purl.obolibrary.org/obo/ENVO_01001023>)))) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<null>))]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000040> [SubClassOf(<http://purl.obolibrary.org/obo/UBERON_0000465> <http://purl.obolibrary.org/obo/BFO_0000040>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) Versio
nIRI(<null>))]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000040> [SubClassOf(<http://purl.obolibrary.org/obo/PO_0025131> <http://purl.obolibrary.org/obo/BFO_0000040>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI
(<null>))]
Use of undeclared class: <http://purl.obolibrary.org/obo/BFO_0000040> [SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_1> <http://purl.obolibrary.org/obo/BFO_0000040>) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIR
I(<null>))]
Use of undeclared annotation property: <http://www.geneontology.org/formats/oboInOwl#inSubset> in annotation [Annotation(<http://www.geneontology.org/formats/oboInOwl#inSubset> "envoPolar") in AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <h
ttp://purl.obolibrary.org/obo/CHEBI_76413> "envoPolar")]
Use of undeclared annotation property: <http://xmlns.com/foaf/0.1/homepage> in annotation [Annotation(<http://xmlns.com/foaf/0.1/homepage> "http://environmentontology.org/"^^xsd:anyURI) in null]
Use of undeclared annotation property: <http://usefulinc.com/ns/doap#bug-database> in annotation [Annotation(<http://usefulinc.com/ns/doap#bug-database> "https://github.com/EnvironmentOntology/envo/issues/"^^xsd:anyURI) in null]

PROFILE VIOLATION ERROR http://purl.obolibrary.org/obo/envo.owl violates profile DL
For details see: http://robot.obolibrary.org/validate-profile#profile-violation-error
java.lang.Exception: validate-profile#PROFILE VIOLATION ERROR http://purl.obolibrary.org/obo/envo.owl violates profile DL
        at org.obolibrary.robot.ValidateProfileCommand.execute(ValidateProfileCommand.java:115)
        at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
        at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
        at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
        at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:61)

[cmungall]

This is actually a false positive, for arcane owlapi reasons

I recommend running robot through makefile targets which will do any necessary preprocessing:

this succeeds:

✗ make validate-dl-profile
robot --catalog catalog-v001.xml merge -i envo-edit.owl -I http://purl.obolibrary.org/obo/ro.owl convert -f ofn -o tmp/validate.ofn

robot --catalog catalog-v001.xml validate-profile --profile DL -i tmp/validate.ofn
OWL 2 DL Profile Report: [Ontology and imports closure in profile]

Basically it's necessary to do a merge step before running validate-profile, see ontodev/robot#1040

[matentzn]

I had already implemented CI for this in ENVO: #1334