On 01/03/13 10:50, [email protected] wrote:
Dear Dave,
thanks for your help! Using OWL_MEM works as expected, just takes longer
to create the OntModel, but it is still acceptable timewise.
OWL_MEM, like RDFS_MEM, does not include any reasoning and there should
be zero difference in time to create.
If you are reporting subjective time when first starting your app then
you are probably just seeing the java class loader pulling in a few more
classes. However, once your app is running the time to wrap an OntModel
with no inference should be very very small and pretty much identical
whichever profile you use.
I was trying to use the least expensive OntModelSpec and started with
RDFS_MEM, just to see if it would return OntClasses. And since it did, I
just got stuck in the wrong path ...
As I say, there is no difference in expense.
I am still curious, why the OntClass instantiation works for "Neoplasm",
but not for "T1_Stage_Finding". Could you please ellaborate a bit more
on what exactly (might have) happened? Here are some things that I still
find confusing:
So based on our email exchange:An OntClass does not necessarily need to
be an owl:Class. When using RDFS_MEM, rdfs:Class would be enoughfor an
OntClass instantiation? What I find confusing is that the exception I
got when using RDFS_MEM refers to "owl:Class or similar". This implies
that OntClass always knows about owl:Classand is checking for it even if
I am using RDFS_MEM. So an rdfs:Class should never be enough for an
OntClass? Even if there was an rdfs:Class statement for Neoplasm, it
should not work since it is not equivalent to owl:Class?
The OntAPI was created at a time there were lots of different Ontology
flavours - there was DAML, there RDFS, there was OWL being developed
which in turn had three profiles.
These days DAML is gone, OWL is by far the most common. People working
in pure RDFS often just work at the RDF level anyway, the OntAPI buys
them less.
So the error message from OntClass is trying to be helpful since the
vast majority of people seem to work with an OWL profile. But it does
not imply that something different is being done under the hood.
To be an OntClass in an RDFS profile you need a rdf:type rdfs:Class.
To be an OntClass in an OWL profile you need a rdf:type owl:Class.
Without inference these, I believe, need to be explicit. Ian can correct
me if I'm wrong on that.
I take it that RDFS_MEM does not do any additional reasoning, so the
statement that makes the OntClass instantiation succeed for "Neoplasm"
must be readily visible. The Thesaurus.owl file does not contain any
mention of rdfs:Class anywhere. I also attached the result of the Sparql
query "SELECT * WHERE { nci:Neoplasm ?p ?s. }". The result shows that
there are no rdfs:Class triples. Theonly rdfs: triples are rdfs:label
and rdfs:subClassOf. rdfs:subClassOf leads to other owl:Classes. And the
other triples describe properties.
I can't explain that. As I said in my message the mystery is why
Neoplasm should have worked for you in an RDFS_MEM profile, not why the
others didn't.
Is there more to how OntClass
determines if it can convert a resource?
Not that I'm aware of but others can answer definitively.
Dave
-----Original Message-----
From: Dave Reynolds <[email protected]>
To: users <[email protected]>
Sent: Mon, Feb 25, 2013 6:21 pm
Subject: Re: OntModel.getOntClass does not return existing classes
On 25/02/13 17:04,[email protected] wrote:
I am using
_modelOnt = ModelFactory.createOntologyModel(OntModelSpec.RDFS_MEM,
ds.getDefaultModel());
Ah, that explains it!
So RDFS inferenceand not OWLbecause I want to keep the loading time to a
minimum. I tried OWL_MICRO_MEM but that a long time to load. I canceled
it after 1 hoursince that is not feasiblefor me.
I can see that you don't want OWL inference.
But what you specified is an *RDFS* profile, not an OWL profile, with no
inference at all.
So the OntAPI has been told that classes are of type rdfs:Class and
there's no inference specified to allow it to deduce that something
which is declared as a owl:Class is also an rdfs:Class.
Use OntModelSpec.OWL_MEM which is an *OWL* profile with no inference.
I can get an OntClass from this model for certain concepts using RDFS
inference, e.g. "Neoplasm", but cannot for others, e.g.
"T1_Stage_Finding". I attached both definitions, directly copied from
the thesaurus.owl file. There must be something different in there that
I don't see.
My neither but now the mystery is why it doesn't complain about
#Neoplasm rather than why it does complain about #T1_Stage_Finding.
I wonder if there are other statements about #Neoplasm in your data
which assert it's an rdfs:Class.
Ialso created a smaller test ontology with just those concepts and
properties from the thesaurus that are required to mirror this
scenario(including parent concepts) and strangely enough, neither of the
two concepts can be retrieved as OntClass.
So that's consistent and reinforces the hypothesis that there's other
statements about #Neoplasm elsewhere in your data.
Dave
-Wolfgang
-----Original Message-----
From: Dave Reynolds <[email protected]>
To: users <[email protected]>
Sent: Mon, Feb 25, 2013 2:00 pm
Subject: Re: OntModel.getOntClass does not return existing classes
On 25/02/13 12:03,[email protected] wrote:
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?
Does look very odd.
Is there any inference involved or is this a plain model?
What OnModelSpec are you using? Clearly if you specified RDFS and had
no inference then the call would fail, though I assume you are using an
OWL spec.
Dave
