Tightening QC on ENVO CI

[matentzn]

For the future

[matentzn]

@kaiiam

[cmungall]

I don't understand how this passed, I see:

OWL 2 DL Profile Report: Ontology and imports closure NOT in profile. The following violations are present:
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> ObjectSomeValuesFrom(<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/CHEBI_155827> [SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001877> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> ObjectUnionOf(<http://purl.obolibrary.org/obo/CHEBI_134024> <http://purl.obolibrary.org/obo/CHEBI_155827> <http://purl.obolibrary.org/obo/CHEBI_29238> <http://purl.obolibrary.org/obo/CHEBI_30218> <http://purl.obolibrary.org/obo/CHEBI_30496> <http://purl.obolibrary.org/obo/CHEBI_36927>))) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo.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> <http://purl.obolibrary.org/obo/GO_0019332> "envoPolar")]
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> ObjectSomeValuesFrom(<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://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]
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> <http://purl.obolibrary.org/obo/CHEBI_76413> "envoPolar")]
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(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<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 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> <http://purl.obolibrary.org/obo/PCO_0000002> "envoPolar")]
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 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> <http://purl.obolibrary.org/obo/GO_0019411> "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> <http://purl.obolibrary.org/obo/GO_0019331> "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://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_24431> <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 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> <http://purl.obolibrary.org/obo/GO_0019409> "envoPolar")]
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>) VersionIRI(<null>))]
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>) VersionIRI(<null>))]
Use of undeclared class: <http://purl.obolibrary.org/obo/CHEBI_155903> [SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03510060> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/CHEBI_155903>)) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo.owl>) VersionIRI(<null>))]
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(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/envo_bridge.owl>) VersionIRI(<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>) 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> <http://purl.obolibrary.org/obo/GO_0019412> "envoPolar")]
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> ObjectSomeValuesFrom(<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://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> <http://purl.obolibrary.org/obo/GO_0019414> "envoPolar")]
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>) VersionIRI(<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>) 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> <http://purl.obolibrary.org/obo/GO_0015948> "envoPolar")]
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/CHEBI_166975> [SubClassOf(<http://purl.obolibrary.org/obo/ENVO_03510061> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002473> <http://purl.obolibrary.org/obo/CHEBI_166975>)) in OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo.owl>) VersionIRI(<null>))]
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> ObjectSomeValuesFrom(<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://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> <http://purl.obolibrary.org/obo/GO_0015979> "envoPolar")]

[matentzn]

BecauSe of a hack. ENVO is Managed in some crappy syntax (RDF XML) and using ofn injects declarations.. this error is so frequent for ODK we decided to ignore it by serialising to ofn first.

[kaiiam]

Isn't RDF XML (owl) the standard syntax that all ODK projects write the final version of the owl to?

I guess the above OWL 2 DL Profile Report is from a profile we normally don't check? I thought we were using elk which misses DL profile material is that correct? If so that explains why we've missed the above.

[matentzn]

DL profile errors are syntactic errors of the OWL file - some of which effect reasoning, but mostly it is about checking if the OWL file is "legal OWL".

RDFXML is the standard export format, because it is the most widely supported serialisation for downstream tools. But it is very bad for editing ontologies - ODK, for example, uses ofn for that. It is easier to diff.