[Pellet-Users] Abstract syntax DifferentIndividuals

[Alan Ruttenberg]

Not winning for me. Using the code I sent earlier I get, for your  
sample ontology, the rdf below. This using the econn-owlapi in in  
swoop-svn-trunk updated today. My class path is all the jars in a  
recent pellet nightly, except that I replaced the econn-owlapi jars  
with those in the newly updated swoop svn.

I can't get it to load into swoop either. I cut out the sample, put  
it into a file called test2.txt, and then used the load ontology menu  
to try to load it.
Keep getting

java.lang.NullPointerException
	at org.semanticweb.owl.model.helper.OntologyHelper.addImportsTo 
(OntologyHelper.java:100)
	at org.semanticweb.owl.model.helper.OntologyHelper.importClosure 
(OntologyHelper.java:94)
	at org.mindswap.swoop.SwoopModel.addOntology(SwoopModel.java:723)
         ...

Could you tell me exactly what you did with what to get your example  
to work? Or could you recommend an appropriate way to  
programmatically load an abstract syntax file into pellet?

Thanks,
Alan


"<?xml version=\"1.0\"?>
<!DOCTYPE owl [
<!ENTITY owl  \"http://www.w3.org/2002/07/owl#\">
<!ENTITY xsd  \"http://www.w3.org/2001/XMLSchema#\">
<!ENTITY rdf \"http://www.w3.org/1999/02/22-rdf-syntax-ns#\">
<!ENTITY rdfs \"http://www.w3.org/2000/01/rdf-schema#\">
]>
<rdf:RDF
xmlns:cas=\"http://www.biopax.org/xref/cas*\"
xmlns:dc=\"http://purl.org/dc/elements/1.1/\"
xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"
xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"
xmlns:owl=\"http://www.w3.org/2002/07/owl#\"
xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"
 >
<owl:Ontology rdf:about=\"http://ex.org\">
</owl:Ontology>
<owl:Class rdf:about=\"http://www.w3.org/2002/07/owl#Thing\">
</owl:Class>


<rdf:Description rdf:about=\"http://www.biopax.org/xref/cas*146-80-5\">
   <rdf:type>
     <owl:Class rdf:about=\"http://www.w3.org/2002/07/owl#Thing\">
     </owl:Class>
   </rdf:type>
</rdf:Description>
<rdf:Description rdf:about=\"http://www.biopax.org/xref/cas*146-80-6\">
   <rdf:type>
     <owl:Class rdf:about=\"http://www.w3.org/2002/07/owl#Thing\">
     </owl:Class>
   </rdf:type>
</rdf:Description>
<rdf:Description rdf:about=\"http://www.biopax.org/xref/cas*146-80-7\">
   <rdf:type>
     <owl:Class rdf:about=\"http://www.w3.org/2002/07/owl#Thing\">
     </owl:Class>
   </rdf:type>
</rdf:Description>
<rdf:Description rdf:about=\"http://www.biopax.org/xref/cas*146-80-8\">
   <rdf:type>
     <owl:Class rdf:about=\"http://www.w3.org/2002/07/owl#Thing\">
     </owl:Class>
   </rdf:type>
</rdf:Description>

</rdf:RDF>


On Feb 15, 2006, at 8:21 AM, Bijan Parsia wrote:

> Alan,
>
> I wasn't able to load your ontology successfully into Swoop (Ron!),  
> but I was able to do:
>
> Namespace(rdf	= <http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
> Namespace(xsd	= <http://www.w3.org/2001/XMLSchema#>)
> Namespace(rdfs	= <http://www.w3.org/2000/01/rdf-schema#>)
> Namespace(owl	= <http://www.w3.org/2002/07/owl#>)
>
> Ontology( <http://ex.org>
>
>  Class(owl:Thing partial)
> Individual(<http://www.biopax.org/xref/cas*146-80-5> type(owl:Thing))
> Individual(<http://www.biopax.org/xref/cas*146-80-6> type(owl:Thing))
> Individual(<http://www.biopax.org/xref/cas*146-80-7> type(owl:Thing))
> Individual(<http://www.biopax.org/xref/cas*146-80-8> type(owl:Thing))
> DifferentIndividuals(<http://www.biopax.org/xref/cas*146-80-5>  
> <http://www.biopax.org/xref/cas*146-80-6> <http://www.biopax.org/ 
> xref/cas*146-80-7> <http://www.biopax.org/xref/cas*146-80-8> )
> )
>
>
> And I got the differentFrom in the concise format and this RDF/XML:
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE rdf:RDF [
>   <!ENTITY ex "http://ex.org">
>   <!ENTITY owl "http://www.w3.org/2002/07/owl#">
>   <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
>   <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
> ]>
> <rdf:RDF xml:base="&ex;"
>          xmlns:owl="&owl;"
>          xmlns:rdf="&rdf;">
>
> <!-- Ontology Information -->
>   <owl:Ontology rdf:about=""/>
>
> <!-- Instances -->
>   <owl:Thing rdf:about="http://www.biopax.org/xref/cas*146-80-5"/>
>   <owl:Thing rdf:about="http://www.biopax.org/xref/cas*146-80-6"/>
>   <owl:Thing rdf:about="http://www.biopax.org/xref/cas*146-80-7"/>
>   <owl:Thing rdf:about="http://www.biopax.org/xref/cas*146-80-8"/>
>   <owl:AllDifferent>
>     <owl:distinctMembers rdf:parseType="Collection">
>       <rdf:Description rdf:about="http://www.biopax.org/xref/ 
> cas*146-80-5"/>
>       <rdf:Description rdf:about="http://www.biopax.org/xref/ 
> cas*146-80-6"/>
>       <rdf:Description rdf:about="http://www.biopax.org/xref/ 
> cas*146-80-7"/>
>       <rdf:Description rdf:about="http://www.biopax.org/xref/ 
> cas*146-80-8"/>
>     </owl:distinctMembers>
>   </owl:AllDifferent>
> </rdf:RDF>
>
> (Ron, the AbstractSyntax entity renderer doesn't get this).
>
> Can you try this simplified example? Perhaps you have an older  
> version of econn-owlapi, or perhaps there's some other problem with  
> your ontology.
>
> Cheers,
> Bijan.
>