Hi Dave,
I am still having issues coming to terms with what is going on in my project. I
am using this source code to get a resource by its "code":
AnnotationProperty codeProp =
_modelOnt.getAnnotationProperty(NS_NCI_HASH + "code");
Literal codeLiteral = _modelOnt.createTypedLiteral(code);
StmtIterator iter = _modelOnt.listStatements(new
SimpleSelector(null, codeProp, codeLiteral));
OntClass diseaseClass = null;
while(iter.hasNext()){
Statement stmt = iter.next();
PrintStatementIterator(stmt.getSubject().listProperties());
diseaseClass = stmt.getSubject().as(OntClass.class);
break;
}
return diseaseClass;
The call to my print method outputs this:
[http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#T1_Stage_Finding,
http://www.w3.org/1999/02/22-rdf-syntax-ns#type,
http://www.w3.org/2002/07/owl#Class]
[http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#T1_Stage_Finding,
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Preferred_Name, "T1 Stage
Finding"^^http://www.w3.org/2001/XMLSchema#string]
[http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#T1_Stage_Finding,
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Semantic_Type,
"Finding"^^http://www.w3.org/2001/XMLSchema#string]
[http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#T1_Stage_Finding,
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#DEFINITION,
"<ncicp:ComplexDefinition
xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#";><ncicp:def-definition>A
clinical and/or pathologic primary tumor TNM finding indicating that the
cancer is limited to the site of
growth.</ncicp:def-definition><ncicp:def-source>NCI</ncicp:def-source></ncicp:ComplexDefinition>"^^http://www.w3.org/1999/02/22-rdf-syntax-ns#XMLLiteral]
The stmt.getSubject().as(OntClass.class) call throws this exception:
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#T1_Stage_Finding to
OntClass: it does not have rdf:type owl:Class or equivalent
The first line from listProperties() states that the resource is an owl:Class.
But the exception begs to differ. I am not using any manually created URIs in
this example and the selector finds a hit for the supplied code (e.g.
"C48720").
What am I missing?
Regards,
Wolfgang
-----Original Message-----
From: Dave Reynolds <[email protected]>
To: users <[email protected]>
Sent: Fri, Feb 22, 2013 6:04 pm
Subject: Re: OntModel.getOntClass does not return existing classes
Sounds like you have an underlying problem with your data or your code.
The URIs you are using when getting the OntClass are not the correct
URIs, or at least are not the same as the ones in the data you are
loading. If listProperties() says there are no values then there no
values, including no rdf:type values, which is consistent with OntClass
complaining.
It's true you can go ahead and assert new values about these URIs but if
they are not the right ones that may lead you into problems later.
Dave
On 22/02/13 16:23, [email protected] wrote:
> Hi,
>
> I re-imported the entire TDB store multiple times (using the windows .bat
files) and also tried an older version that I loaded with the CYGWIN bash
scripts some time ago. Still no success in getting some of the classes as
OntClass.
>
> So I tried OntModel.setStrictMode(false). And that returns an OntClass
> object.
But unfortunately listProperties() and most other methods on that object return
empty results. I also tried comparing some results of isXXX methods. isClass()
is true, but the rest pretty much returns false where the other ones return
true.
>
>
> My goal is to insert individuals of these classes. I tried that with these
objects and surprisingly enough it works fine. Great!
>
> So I should be good to go unless I want to use these objects for further
relationship investigation (e.g. via properties)?
>
> Regards,
> Wolfgang
>
> P.S.: I could share my TDB store and the NCIt file I am using via dropbox or
similar if somebody wanted to re-create the problem.
>
>
>
>
> -----Original Message-----
> From: hueyl16 <[email protected]>
> To: users <[email protected]>
> Sent: Thu, Feb 21, 2013 6:36 pm
> Subject: Re: OntModel.getOntClass does not return existing classes
>
>
> Hi Dave,
>
> I am using an older version of the NCI thesaurus (11.12e) where the URIs still
> contain meaningful names. It is still available on the NCIt download page.
>
> I am sure the URIs I am using are correct, since it works in my sparql queries
> and the listProperies() call.
>
> I am going to give your suggestion a shot tomorrow.
>
> Another piece of info: I recently switched to the latest Jena version and am
now
> using the windows batch files for TDB import instead of the CYGWIN/bash based
> versions that I used before. Unfortunately, I have not really used the JENA
API
> before. I was strictly using Sparql queries so I cannot really tell if that
> might be the culprit.
>
> Btw, I am really happy that the windows batch files were added.
>
> Thanks!
> Wolfgang
>
>
>
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: Dave Reynolds <[email protected]>
> To: users <[email protected]>
> Sent: Thu, Feb 21, 2013 6:26 pm
> Subject: Re: OntModel.getOntClass does not return existing classes
>
>
>
> On 21/02/13 16:46, [email protected] wrote:
>>
>> Hi,
>>
>> I imported the NCI Thesaurus into a TDB store. I am using the Jena API to get
> references to existing classes. This is my basic setup:
>>
>> Dataset ds =
>> TDBFactory.createDataset("C:\\Playground\\Ontology\\TDBStore_Instances");
>> OntModel modelOnt = ModelFactory.createOntologyModel(OntModelSpec.RDFS_MEM,
> ds.getDefaultModel());
>>
>> For some classes the getOntClass() method works fine, e.g.:
>>
>> modelOnt.getOntClass(NS_NCI_HASH + "Neoplasm");
>> modelOnt.getOntClass(NS_NCI_HASH + "Volume");
>>
>> But for other classes, getOntClass() returns , e.g.:
>>
>> modelOnt.getOntClass(NS_NCI_HASH + "Carcinoma");
>> modelOnt.getOntClass(NS_NCI_HASH + "Malignant_Prostate_Neoplasm");
>>
>>
>> I tried to get an OntClass reference for these in different ways, too, e.g.:
>> I used modelOnt.listStatements(...) and stmt.getSubject().as(OntClass.class).
> But this throws the exception:
>>
>> Cannot convert node
>> http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Malignant_Prostate_Neoplasm
>
> to OntClass: it does not have rdf:type owl:Class or equivalent
>>
>> The problem is, that
>> http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Malignant_Prostate_Neoplasm
>
> is an owl:Class. I verified this by just printing
> stmt.getSubject().listProperties()
>
> to the console:
>>
>> [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Malignant_Prostate_Neoplasm,
>
> http://www.w3.org/1999/02/22-rdf-syntax-ns#type,
> http://www.w3.org/2002/07/owl#Class]
>>
>> I also used a Sparql query on the same data set:
>>
>> String query = PREFIXES
>> + " SELECT * "
>> + " WHERE { "
>> + " nci:Malignant_Prostate_Neoplasm ?p ?o . "
>> + " }";
>>
>> Which prints this:
>> p | o
>> rdf:type | owl:Class
>> nci:Preferred_Name | "Malignant Prostate Neoplasm"^^xsd:string
>> ...
>>
>> So based on what I can see (and know), Carcinoma and
>> Malignant_Prostate_Neoplasm
>
> are both owl:Class, but getOntClass() does not seem to agree.
>>
>> Does anybody know why?
>
> No :)
>
> If your subject resource really does have an rdf:type owl:Class
> assertion then that's enough to allow the as(OntClass.class) to go through.
>
> If I download that ontology I don't see URIs like that, they are all of
> the form #Cxxxxxx so it's hard to check. Presumably you have do some
> sort of transformation on the data.
>
> If you really are using identical URIs in the getOntClass and the
> listStatments call then I can't see how that could happen. Short of
> something drastic like a corrupt TDB database but you would know about that.
>
> You do have the workaround to setStrictMode(false). Perhaps if you do
> that and then examine the OntClass you get back some explanation might
> be revealed.
>
> Dave
>
>
>
>
>
>
>
>
>
