ejp-rd-vp / CDE-semantic-model

Semantic data model of the set of common data elements for rare disease registration
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Imports missing from example data #101

Open henrietteharmse opened 2 years ago

henrietteharmse commented 2 years ago

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:

image

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:

image

pabloalarconm commented 1 year ago

Hi @henrietteharmse sorry for this late response, Im been checking any issues at the last stable CDE version (2.0.0). I would appreciate if you could check if you have noticed the same problem with this new coming version. This is an exemplar rdf from the same data element: Status data

Bests, Pablo