如何使用 OWL API 从每个 <rdf:Description> 中检索 <oboInOwl:hasExactSynonym>

Question

我是 OWL API 的新手，因此我在检索数据时遇到了一些问题。

假设我有以下数据：

<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 (e.g. 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>

对于每个 "rdf:description" 我想使用 OWL API 在 java。

到目前为止，我可以获得所有标签，但无法获得关于哪个标签对应哪个描述的链接。

目前我的代码如下所示：

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);
                }
            }

        }

有人可以帮我解决这个问题吗？

Answer 1

这应该有帮助：

    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);
        }
    }

这两个映射保存 IRI（在这种情况下注释主题始终是 IRI - 注释附加到类的 IRI，而不是类本身）和值之间的关系一个属性。如果将标签值与某个IRI的属性的值进行匹配，则可以通过映射中的IRI找到另一个值

如何使用 OWL API 从每个 <rdf:Description> 中检索 <oboInOwl:hasExactSynonym>

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

java

owl

ontology

owl-api