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In chatting to @rajaram5 I was very perplexed to note that object properties are noted as annotations in Protege. As an example, see patientStatus.ttl which looks as follows in Protege:
The perplexing part is that SIO_000217 and SIO_000228 are noted as annotations rather than object properties. For example, this is how SIO_000217 is defined:
<rdf:Description rdf:about="http://semanticscience.org/resource/SIO_000217">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/>
<rdfs:subPropertyOf rdf:resource="http://semanticscience.org/resource/SIO_000223"/>
<owl:inverseOf rdf:resource="http://semanticscience.org/resource/SIO_000218"/>
<rdfs:range rdf:resource="http://semanticscience.org/resource/SIO_000005"/>
<dct:description xml:lang="en">has quality is a relation between an entity and the quality that it bears.</dct:description>
<rdfs:label xml:lang="en">has quality</rdfs:label>
<dc:identifier>SIO_000217</dc:identifier>
<rdfs:isDefinedBy rdf:resource="http://semanticscience.org/ontology/sio.owl"/>
</rdf:Description>
The reason why Protege sees these annotation properties rather than object properties is because the imports are missing. For patientStatus.ttl this can be corrected by adding the following imports:
<http://purl.org/ejp-rd/cde/v020/example-rdf/> rdf:type owl:Ontology ;
owl:imports <http://purl.obolibrary.org/obo/obi.owl> ,
<http://semanticscience.org/ontology/sio.owl> .
In Protege this will then be displayed correctly as object properties:
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