ro.obo is highly incomplete

[matentzn]

There are a few things in RO that cannot be captured in RO:

• SubAnnotationPropertyOf axioms
• AnnotationPropertyRange axioms
• DLSafeRules
• SubObjectPropertyOf if they involve inverses
• Complex subClassOf axioms beyond OBO
• Complex disjoint class axioms
• Some OP characteristics, like IrreflexiveObjectProperty
• ObjectPropertyRange axioms with complex ranges
• DataPropertyRange axioms (?)

All in all there are 147 axioms squished into the owl-axioms header of ro.obo.

Stuff dropped from ro.obo

``` SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) AnnotationPropertyRange( xsd:nonNegativeInteger) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) SubAnnotationPropertyOf( ) ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) ObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ObjectSomeValuesFrom( )) ObjectPropertyRange( ObjectSomeValuesFrom( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) IrreflexiveObjectProperty() SubObjectPropertyOf( ObjectInverseOf()) ObjectPropertyRange( ObjectSomeValuesFrom( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) IrreflexiveObjectProperty() IrreflexiveObjectProperty() ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) ObjectPropertyRange( ObjectUnionOf( )) IrreflexiveObjectProperty() IrreflexiveObjectProperty() IrreflexiveObjectProperty() IrreflexiveObjectProperty() DataPropertyRange( DatatypeRestriction(xsd:short xsd:minInclusive \"0\"^^xsd:short xsd:maxInclusive \"100\"^^xsd:short)) SubClassOf( owl:Thing) DisjointClasses( ObjectSomeValuesFrom( )) SubClassOf( owl:Thing) DisjointClasses( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) DisjointClasses( ObjectSomeValuesFrom( )) SubClassOf( owl:Thing) SubClassOf( ObjectHasSelf()) SubClassOf( owl:Thing) SubClassOf( owl:Thing) SubClassOf( ObjectHasSelf()) SubClassOf( owl:Thing) SubClassOf( ObjectHasSelf()) SubClassOf( owl:Thing) SubClassOf( owl:Thing) SubClassOf( owl:Thing) SubClassOf(owl:Nothing owl:Nothing) SubClassOf( owl:Thing) SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(

[matentzn]

There is a second problem here though:

owltools --use-catalog ro.owl --merge-import-closure -o -f obo ro.obo.tmp && mv ro.obo.tmp ro.obo

$ grep OMO_ ro.owl
    <!-- http://purl.obolibrary.org/obo/OMO_0002000 -->
    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0002000"/>
        <obo:OMO_0002000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
}</obo:OMO_0002000>
        <obo:OMO_0002000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
}</obo:OMO_0002000>
        <obo:OMO_0002000 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
}</obo:OMO_0002000>
$grep OMO: ro.obo
NO OUTPUT

In other words, the OMO annotations entirely disappear cycling through owltools.

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