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
