Re: [OWLAPI-developer] Impossible to "load" all classes

[Ignazio P. <ipa...@gm...>]

On 30 October 2013 22:49, Alessandro Solimando
<ale...@gm...> wrote:
> Dear owl-api list,
> in my project I need to load ontologies and alignments between them.
>
> In order to sanity check the mappings I need to check if the mapped
> classes do exist in the pair of input ontologies.
>
> To this aim, I am iterating on ontology.getClassesInSignature(), but I
> am missing some classes, here is the code snippet:
>
> // computes nodes from concepts
> Set<OWLClass> classes = o.getClassesInSignature();
> Iterator<OWLClass> itr = classes.iterator();
> OWLClass cls;
> while(itr.hasNext()){
> cls = itr.next();
> createVertex(cls);
> }
>
> While trying OAEI 2012 alignments (anatomy track) on human and mouse
> ontologies (available here:
> http://oaei.ontologymatching.org/2012/anatomy/anatomy-dataset.zip) I
> found that none of the declared classes
> with IRI prefix equals to
> "http://www.geneontology.org/formats/oboInOwl#" were loaded, for
> instance "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"
> (in mouse.owl ontology).


I cannot reproduce your issue. The output I get is:

TestAlessandro.main()
<http://www.geneontology.org/formats/oboInOwl#DbXref>
OntologyID(OntologyIRI(<http://mouse.owl>))
TestAlessandro.main()
<http://www.geneontology.org/formats/oboInOwl#SynonymType>
OntologyID(OntologyIRI(<http://mouse.owl>))
TestAlessandro.main()
<http://www.geneontology.org/formats/oboInOwl#Definition>
OntologyID(OntologyIRI(<http://mouse.owl>))
TestAlessandro.main()
<http://www.geneontology.org/formats/oboInOwl#ObsoleteClass>
OntologyID(OntologyIRI(<http://mouse.owl>))
TestAlessandro.main()
<http://www.geneontology.org/formats/oboInOwl#Synonym>
OntologyID(OntologyIRI(<http://mouse.owl>))
TestAlessandro.main()
<http://www.geneontology.org/formats/oboInOwl#Subset>
OntologyID(OntologyIRI(<http://mouse.owl>))

for this code:

 public static void main(String[] args) throws OWLOntologyCreationException {
        OWLOntology o =
OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new
File("anatomy-dataset/mouse.owl"));
        for (OWLOntology ont : o.getImportsClosure()) {
            for (OWLClass c : ont.getClassesInSignature()) {
                if (c.toString().contains("obo")) {
                    System.out.println("TestAlessandro.main() " + c +
" \t" + ont.getOntologyID());
                }
            }
        }
    }

This is with the latest snapshot and with 3.4.3.

>
> Even if I do not think it is an imported class, I tried to check also
> imported ontologies (using getImports() method of OWLOntologyManager),
> but with no effect.
>
> I tried with Protege 4.2 and it is actually able to load the classes
> (I was not able to find the bit of code performing this loading,
> though), so I know that I am missing something, but I am not able to
> fix this.
>
> Of course I checked loading configuration and all the other classes
> that seemed related to me, but without any luck.
>
> I am using OWL-API version 3.4.3 (that I would like to stick to, at
> least for the moment).


Do you have any specific reason for this? There have been bug fixes in
the meantime that you'll be missing :-)
HTH
I.

>
> Do you have any suggestion?
>
> Thanks in advance,
> Alessandro
>
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