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RDFBones / RDFBones-O

An RDF ontology for research data from physical anthropology and related fields of expertise.
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Reasoner Error #94

Closed kdaveed closed 7 years ago

kdaveed commented 7 years ago

The reasoner in VIVO gives the following error msg:

org.semanticweb.owlapi.reasoner.ReasonerInternalException: Non simple role used as simple: http://purl.obolibrary.org/obo/BFO_0000050

if the RDFBones.owl contains restriction on the property : http://purl.obolibrary.org/obo/BFO_0000050.

zarquon42b commented 7 years ago

Can you upload a screenshot of the error? Can you access the VIVO UI?

cuboideum commented 7 years ago

@kdaveed Can you also paste the relevant lines from the logfile, please?

kdaveed commented 7 years ago

This is the only one line regarding the reasoner error in the log file:

_[JFactTBoxReasoner] org.semanticweb.owlapi.reasoner.ReasonerInternalException: Non simple role used as simple: http://purl.obolibrary.org/obo/BFO_0000050_

And the screenshot:

screen shot 2016-12-15 at 13 42 30

kdaveed commented 7 years ago

It is strange because the other properties in the restrictions do not cause exceptions. Also if the restrictions on the property _http://purl.obolibrary.org/obo/BFO_0000050_ are commented out then it works.

zarquon42b commented 7 years ago

Commented in which file?

kdaveed commented 7 years ago

In the RDFBones.owl

cuboideum commented 7 years ago

There are three simple restrictions on obo:BFO_0000050 in RDFBones-O.owl:

<owl:Class rdf:about="http://w3id.org/rdfbones/core#SkeletalMaterialRequirement">
   <rdfs:subClassOf>
      <owl:Restriction>
         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
         <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0001896"/>
      </owl:Restriction>
   </rdfs:subClassOf>
</owl:Class>

<owl:Class rdf:about="http://w3id.org/rdfbones/core#SkeletalMaterialSpecification">
   <rdfs:subClassOf>
      <owl:Restriction>
         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
         <owl:allValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0000260"/>
      </owl:Restriction>
   </rdfs:subClassOf>
   <rdfs:subClassOf>
      <owl:Restriction>
         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
         <owl:cardinality rdf:datatype="http://www.w3.org2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
      </owl:Restriction>
   </rdfs:subClassOf>
</owl:Class>

@kdaveed Did you comment them all out? It would be great if you could try them out separately in order to narrow down the problem.

kdaveed commented 7 years ago

Yes, I commented out all of them. Okay, then I try them separately.

zarquon42b commented 7 years ago

This seems to be owed to the cardinality constraint (see http://protege-project.136.n4.nabble.com/Dead-reasoner-td4656114.html)

zarquon42b commented 7 years ago

@cuboideum will release a fix in a moment

zarquon42b commented 7 years ago

BTW: it works by removing the cardinality constraint only: RDFBones.owl, line 28594.

kdaveed commented 7 years ago

@zarquon42b, @cuboideum I experienced the same. The problem lies on the following restriction: 

<owl:Restriction>
         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
         <owl:cardinality rdf:datatype="http://www.w3.org2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
zarquon42b commented 7 years ago

Yes, that was what my previous messages intended to say.