How can I retrieve <oboInOwl:hasExactSynonym> from every <rdf:Description> using OWL API

Question

I am new to OWL API hence I am facing some issues for retrieving data.

Suppose I have the following data:

 <rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0044297"> <oboInOwl:creation_date>"2010-02-05T10:37:16Z"</oboInOwl:creation_date> <obo:IAO_0000115>"The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections."</obo:IAO_0000115> <oboInOwl:hasOBONamespace>"cellular_component"</oboInOwl:hasOBONamespace> <oboInOwl:hasDbXref>"Wikipedia:Cell_body"</oboInOwl:hasDbXref> <oboInOwl:hasDbXref>"FMA:67301"</oboInOwl:hasDbXref> <oboInOwl:hasExactSynonym>"cell soma"</oboInOwl:hasExactSynonym> <rdfs:label>"cell body"</rdfs:label> <rdfs:subClassOf>http://purl.obolibrary.org/obo/GO_0044464</rdfs:subClassOf> <oboInOwl:hasDbXref>"FBbt:00005107"</oboInOwl:hasDbXref> <rdf:type>http://www.w3.org/2002/07/owl#Class</rdf:type> <oboInOwl:id>"GO:0044297"</oboInOwl:id> <rdfs:comment>"Note that 'cell body' and 'cell soma' are not used in the literature for cells that lack projections, nor for some cells (eg yeast with mating projections) that do have projections."</rdfs:comment> <oboInOwl:created_by>"xyz"</oboInOwl:created_by> <oboInOwl:inSubset>http://purl.obolibrary.org/obo/go#goslim_pir</oboInOwl:inSubset> </rdf:Description> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0071509"> <oboInOwl:hasRelatedSynonym>"activation of MAPKK activity involved in mating response"</oboInOwl:hasRelatedSynonym> <rdfs:subClassOf>http://purl.obolibrary.org/obo/GO_0090028</rdfs:subClassOf> <oboInOwl:hasOBONamespace>"biological_process"</oboInOwl:hasOBONamespace> <oboInOwl:hasExactSynonym>"activation of MAP kinase kinase activity during conjugation with cellular fusion"</oboInOwl:hasExactSynonym> <oboInOwl:hasExactSynonym>"conjugation with cellular fusion, activation of MAPKK activity"</oboInOwl:hasExactSynonym> <rdfs:label>"activation of MAPKK activity involved in conjugation with cellular fusion"</rdfs:label> <rdf:type>http://www.w3.org/2002/07/owl#Class</rdf:type> <oboInOwl:id>"GO:0071509"</oboInOwl:id> <oboInOwl:creation_date>"2010-01-05T02:09:58Z"</oboInOwl:creation_date> <oboInOwl:hasExactSynonym>"conjugation with cellular fusion, activation of MAP kinase kinase activity"</oboInOwl:hasExactSynonym> <oboInOwl:created_by>"midori"</oboInOwl:created_by> <obo:IAO_0000115>"Any process that initiates the activity of the inactive enzyme MAP kinase kinase in the context of conjugation with cellular fusion."</obo:IAO_0000115> <rdfs:subClassOf>http://purl.obolibrary.org/obo/GO_0000186</rdfs:subClassOf> </rdf:Description> 

For each of the "rdf:description" I want to retrieve its corresponding "rdf:label", "oboInOwl:hasExactSynonym" and "rdfs:subClassOf" using OWL API in java.

So far I can get all labels but not the linkages as to which label is for which description.

Currently my code looks like:

OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLOntology pizzaOntology = manager.loadOntologyFromOntologyDocument(f);
        Set<OWLOntology> allOntologies = manager.getImportsClosure(pizzaOntology);
        //System.out.println(allOntologies);
        OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
        OWLReasoner reasoner = reasonerFactory.createReasoner(pizzaOntology);
        //pizzaOntology
        OWLDataFactory factory = manager.getOWLDataFactory();

        Set<OWLAxiom> axiom = pizzaOntology.getAxioms();
        for (OWLAxiom o : axiom) {
            AxiomType<?> at = o.getAxiomType();
            //System.out.println("Annotation type is "+at+" for "+o);

            if (at == AxiomType.ANNOTATION_ASSERTION) {
                OWLAnnotationAssertionAxiom ax = (OWLAnnotationAssertionAxiom) o;
                //Check if the axiom is a label and write to file
                if(ax.getProperty().toString().contains("hasExactSynonym"))
                System.out.println("Data is "+ax.getValue().toString());
                if (ax.getProperty().equals(factory.getRDFSLabel())) {
                    String label = ax.getValue().toString();
                    label = label.toLowerCase();
                    label = label.replaceAll("[^\\p{L}\\p{Nd}]+", " ");
                    allLabels.add(label);
                }
            }

        }

Can someone help me with some ideas about this?

Answer 1

This should help:

    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
    OWLOntology pizzaOntology = manager.loadOntologyFromOntologyDocument(f);
    Set<OWLOntology> allOntologies = manager.getImportsClosure(pizzaOntology);
    // System.out.println(allOntologies);
    OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
    OWLReasoner reasoner = reasonerFactory.createReasoner(pizzaOntology);
    // pizzaOntology
    OWLDataFactory factory = manager.getOWLDataFactory();
    Map<OWLAnnotationSubject, String> allLabels = new HashMap<>();
    Map<OWLAnnotationSubject, String> allExactSynonyms = new HashMap<>();
    for (OWLAnnotationAssertionAxiom ax : pizzaOntology
        .getAxioms(AxiomType.ANNOTATION_ASSERTION)) {
        // Check if the axiom is a label and write to file
        OWLAnnotationSubject subject = ax.getSubject();
        if (ax.getProperty().toString().contains("hasExactSynonym")) {
            allExactSynonyms.put(subject, ax.getValue().toString());
        }
        if (ax.getProperty().equals(factory.getRDFSLabel())) {
            String label = ax.getValue().toString();
            label = label.toLowerCase();
            label = label.replaceAll("[^\\p{L}\\p{Nd}]+", " ");
            allLabels.put(subject, label);
        }
    }

The two maps hold the relation between an IRI (the annotation subject in this case is always an IRI - annotation are attached to IRIs of classes, not to classes themselves) and the value of a property. If you match the label value with the value of a property for an IRI, you can find the other value through the IRI in the map.