OWL ObjectProperty loading as annotation in Protég

Question

I'm trying to load an ontology in Protégé but it is not processed as expected. Most problematic is that all the Object and Data Properties appear as Annotation instead of Data Property and Object Property.

I have an Object Property kingdom:

<owl:ObjectProperty rdf:about="&wo;kingdom">
    <rdfs:label xml:lang="en">kingdom</rdfs:label>
    <rdfs:comment xml:lang="en">associates a taxon rank with a kingdom</rdfs:comment>
    <vs:term_status>testing</vs:term_status>
    <rdfs:range rdf:resource="&wo;Kingdom"/>
    <rdfs:domain rdf:resource="&wo;TaxonRank"/>
</owl:ObjectProperty>

/nature/life/Chordate#kingdom has the value /nature/life/Animal#kingdom for as its kingdom:

<wo:Phylum rdf:about="/nature/life/Chordate#kingdom">
    <rdfs:label>Vertebrates</rdfs:label>
    <wo:kingdom rdf:resource="/nature/life/Animal#kingdom"/>
</wo:Phylum>

However, in Protégé, the property is showing as an annotation. I do not understand why it is not showing as an object property to kingdom.

Why is this?

Answer 1

It seems to be a bug in Protege. How to fix it:

• Open your file index.rdf with Protege, it takes a bit of time in order to import some files.
• Save the ontology in RDF/XML format, pick the folder when you want to put it and call it ontology.owl. The extension is important, save it as OWL file.
• Close Protege and re-open it, open the file ontology.owl, you should now see the property correctly displayed.

Why is it doing that? I believe Protege gets confused by the .rdf and interprets wrongly the data.

Answer 2

When I save my ontology as RDF/XML format, object property of instance becomes annotations. However, if the ontology is saved as Turtle Syntax, object property will be shown normally when opened with protege again.

Answer 3

If you find that your object properties appear as annotations, the solution is to export as ontology. That will turn your annotations into classes.