Problems to read a owl ontology using Jena

Question

I'm trying to a read a owl ontology using Jena. The ontology was created in Protégé.

This is (part of) my original .owl file (some terms are in Portuguese):

<?xml version="1.0"?>


<!DOCTYPE Ontology [
    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
    <!ENTITY xml "http://www.w3.org/XML/1998/namespace" >
    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
]>


<Ontology xmlns="http://www.w3.org/2002/07/owl#"
     xml:base="http://james.miranda.br/Onto"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     ontologyIRI="http://james.miranda.br/Onto"
     versionIRI="http://james.miranda.br/Onto/1.0.0">
    <Prefix name="" IRI="http://www.w3.org/2002/07/owl#"/>
    <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/>
    <Prefix name="rdf" IRI="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
    <Prefix name="xsd" IRI="http://www.w3.org/2001/XMLSchema#"/>
    <Prefix name="rdfs" IRI="http://www.w3.org/2000/01/rdf-schema#"/>
    <Annotation>
        <AnnotationProperty abbreviatedIRI="rdfs:comment"/>
        <Literal xml:lang="en" datatypeIRI="&rdf;PlainLiteral">Ontology for the decision process</Literal>
    </Annotation>
    <Annotation>
        <AnnotationProperty abbreviatedIRI="rdfs:comment"/>
        <Literal xml:lang="pt" datatypeIRI="&rdf;PlainLiteral">Ontologia para o processo de tomada de decisões.</Literal>
    </Annotation>
    <Declaration>
        <Class IRI="#AcaoDesign"/>
    </Declaration>
    <Declaration>
        <Class IRI="#Alternativa"/>
    </Declaration>

Complete file in PasteBin

This is my class:

public class ReadOntology {


    public static void run(String ontologyInFile) {

        OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF, null);
        InputStream ontologyIn = FileManager.get().open(ontologyInFile);

        loadModel(model, ontologyIn);
    }


    /** 
     * @param m
     * @param ontologyIn */
    protected static void loadModel(OntModel m, InputStream ontologyIn) {
        try {
             m.read(ontologyIn, "RDF/XML");
             //also tried m.read(ontologyIn, "OWL/XML");
        } catch (Exception e) {
            System.out.println(e.getMessage());
        }

    }

}

I'm using this class in my HTTP Servlet class like below:

ServletContext context = this.getServletContext();
String fullPath = context.getRealPath("/WEB-INF/ontology/Onto.owl");
ReadOntology.run(fullPath);

and I was receiving the following error:

log4j:WARN No appenders could be found for logger (org.apache.jena.riot.system.stream.JenaIOEnvironment).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Error [line: 27, col: 64] {E201} Multiple children of property element

I was thinking that the problem was log4j, but the comments in this question took me to another direction.

With a bit of research and attention, I saw in the Ontology API documentation that Jena does not have full support to OWL2, and apparently, this was the problem. The answer for this another question indicated that the solution could be in the .owl file.

Finally, I saved it in RDF/XML (the file extension is still .owl) and the result is:

<?xml version="1.0"?>


<!DOCTYPE rdf:RDF [
    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
]>


<rdf:RDF xmlns="http://www.w3.org/2002/07/owl#"
     xml:base="http://www.w3.org/2002/07/owl"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
    <Ontology rdf:about="http://james.miranda.br/Onto">
        <rdfs:comment xml:lang="en">Ontology for the decision making process</rdfs:comment>
        <rdfs:comment xml:lang="pt">Ontologia para o processo de tomada de decisões.</rdfs:comment>
        <versionIRI rdf:resource="http://james.miranda.br/Onto/1.0.0"/>
    </Ontology>



    <!-- 
    ///////////////////////////////////////////////////////////////////////////////////////
    //
    // Object Properties
    //
    ///////////////////////////////////////////////////////////////////////////////////////
     -->




    <!-- http://james.miranda.br/Onto#atende -->

    <ObjectProperty rdf:about="http://james.miranda.br/Onto#atende">
        <rdf:type rdf:resource="&owl;InverseFunctionalProperty"/>
    </ObjectProperty>



    <!-- http://james.miranda.br/Onto#compoe -->

    <ObjectProperty rdf:about="http://james.miranda.br/Onto#compoe">
        <rdfs:subPropertyOf rdf:resource="http://james.miranda.br/Onto#ehParteDe"/>
    </ObjectProperty>



    <!-- http://james.miranda.br/Onto#conflitaCom -->

    <ObjectProperty rdf:about="http://james.miranda.br/Onto#conflitaCom">
        <rdf:type rdf:resource="&owl;ReflexiveProperty"/>
    </ObjectProperty>

Complete file in PasteBin.

but the same error persists. I found other questions with similar problem, but the solutions did not help me.

I don't know what to do now. What I'm doing wrong?

Information:

Ubuntu 14.04;
JDK 1.8.0;
Netbeans 8.0.2;
GlassFish 4.1;
Jena 3.1.0;

Hi, without getting access to the whole ontology, no way to help. Can you share it somehow? Your code looks ok. And I don't think that Jena will have problems in parsing the ontology, even if there are some OWL2 constructs contained in it. — UninformedUser, Aug 23 '16 at 06:38
Thanks for your comment @AKSW. I put two links for PasteBin with the whole ontology. — James, Aug 26 '16 at 02:54
Thanks. For me loading the ontology works perfectly when I run it within my IDE with Maven dependencies for Apache Jena 3.1.0. (`model.size()` = 1376 triples) . So something else must go wrong. Especially the line number of your error message just contains a bunch of `/` characters for comments, thus, nothing would be parsed here for OWL. Can you run it via a separate main method within your Java project? — UninformedUser, Aug 26 '16 at 09:16
I created the whole project again from the beginning and now it's working, even without any changes in my class. I can't understand it, but thanks for your help anyway, @AKSW — James, Aug 27 '16 at 14:03

score 1 · Accepted Answer · answered Sep 20 '16 at 02:16

Just to inform anyone with a similar problem than mine (or anyone that wants to read a protégé ontology using Jena), below is the process and code that I used to achieve it:

1 - In Protégé, save your file as RDF/XML;

2 - Copy the file to your WEB-INF directory (under any sub-directory if you want);

3 - Create a class to read your ontology. For example:

 import java.io.InputStream;
 import org.apache.jena.ontology.*;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.util.FileManager;

 public class ReadOntology {

    public OntModel model;

    public static void run(String ontologyInFile) {

        model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF, null);
        InputStream ontologyIn = FileManager.get().open(ontologyInFile);

        loadModel(model, ontologyIn);
    }


    /** 
     * @param m
     * @param ontologyIn */
    protected static void loadModel(OntModel m, InputStream ontologyIn) {
        try {
             m.read(ontologyIn, "RDF/XML");
        } catch (Exception e) {
            System.out.println(e.getMessage());
        }

    }

}

4 - Using a Servlet class (that extends HttpServlet), you can use the created class like below:

ServletContext context = this.getServletContext();
String fullPath = context.getRealPath("/WEB-INF/yourOntologyName.owl");
ReadOntology.run(fullPath);
ExtendedIterator<OntClass> classIterator = ReadOntology.model.listClasses(); 
while (classIterator.hasNext()) { 
    OntClass ontClass = classIterator.next(); 
    System.out.println(ontClass.toString());
}

Problems to read a owl ontology using Jena

1 Answers1