retrieve owl file data using Jena

Question

I have the following owl file and want to retrieve the related data to a given class.

<owl:Class rdf:about="http://purl.obolibrary.org/obo/DOID_0001">
            <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DOID_11"/>   
            <obo:IAO_11 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A def def def def.</obo:IAO_0000115> 
            <oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">AA:006394</oboInOwl:hasDbXref>
            <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">abcde</oboInOwl:hasExactSynonym> 
            <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">ABCDEFG</rdfs:label>
        </owl:Class>

For example I wanted to retrieve the subClassOf which should be DOID_11 without success using the following code:

//create the reasoning model using the base
 OntModel inf = ModelFactory.createOntologyModel();

 // use the FileManager to find the input file
 InputStream in = FileManager.get().open(inputFileName);
 if ( in == null) {
     throw new IllegalArgumentException("File: " + inputFileName + " not found");
 }

 inf.read( in , "");

 ExtendedIterator <? > classes = inf.listClasses();
 while (classes.hasNext()) {
     OntClass essaClasse = (OntClass) classes.next();

     System.out.println("Classe: " + essaClasse.getLocalName());
     for (Iterator <? > i = essaClasse.listSubClasses(); i.hasNext();) {

         OntClass c = (OntClass) i.next();
         System.out.print("   " + c.getLocalName() + "\n");
     } // end for 
 }

I get just "DOID_0001" instead of "DOID_0001" and "DOID_11". I need also to get all of the other information such as "" and "

No, you are wrong. The statement in your ontology is DOID_0001 rdfs:subClassOf DOID_11. That means, DOID_11 is the superclass of ` DOID_0001` not vice versa. And if you ask for all subclasses of DOID_0001 it's indeed only the class itself as trivial inference. — UninformedUser
I need just to have the following result: SuperClass: DOID_11, SubClass: DOID_11, Def: A def A def .. , Synonym: abcde, label: ABCDEFG. So I need to retrieve the data as it is in order. — StaOver
Ok, but did you understand that what you expected was wrong? — UninformedUser
There is no order in RDF resp. OWL. An RDF graph is a set of triples and an OWL ontology a set of OWL axioms respectively. You can retrieve all data for a given subject via SPARQL or via a convenience method, see my updated answer — UninformedUser

UninformedUser UninformedUser · Accepted Answer · 2016-07-27T19:37:44

No, you are wrong. The statement in your ontology is

DOID_0001 rdfs:subClassOf DOID_11

That means, DOID_11 is the superclass of DOID_0001 not vice versa. And if you ask for all subclasses of DOID_0001, it's indeed only the class itself as trivial inference.

Update

Statements for each class can be retrieved via

    StmtIterator stmtIterator = inf.listStatements(essaClasse, null, (RDFNode) null);
    while(stmtIterator.hasNext()) {
        Statement st = stmtIterator.next();
        Property p = st.getPredicate();
        RDFNode o = st.getObject();
        System.out.println(p + ":" + o);
    }

retrieve owl file data using Jena

1 Answers

Update