本文整理汇总了Java中org.semanticweb.owlapi.model.OWLClassAxiom类的典型用法代码示例。如果您正苦于以下问题:Java OWLClassAxiom类的具体用法?Java OWLClassAxiom怎么用?Java OWLClassAxiom使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
OWLClassAxiom类属于org.semanticweb.owlapi.model包,在下文中一共展示了OWLClassAxiom类的12个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: hasFilterClass
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
/**
* Check that there is an axiom, which use a class (in its signature) that
* has a ancestor in the root term set.
*
* @param axioms set to check
* @param rootTerms set root of terms
* @return boolean
*/
private boolean hasFilterClass(Set<OWLClassAxiom> axioms, Set<OWLClass> rootTerms) {
if (axioms != null && !axioms.isEmpty()) {
for (OWLClassAxiom ax : axioms) {
if (ax instanceof OWLEquivalentClassesAxiom) {
Set<OWLClass> signature = ax.getClassesInSignature();
for (OWLClass sigCls : signature) {
NodeSet<OWLClass> superClasses = reasoner.getSuperClasses(sigCls, false);
for(OWLClass root : rootTerms) {
if (superClasses.containsEntity(root)) {
return true;
}
}
}
}
}
}
return false;
}
开发者ID:owlcollab,项目名称:owltools,代码行数:27,代码来源:CommandRunner.java
示例2: testSpecies
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
private void testSpecies(OWLOntology ontology) {
IRI iri = IRI.create("http://purl.obolibrary.org/obo/NCBITaxon_species");
OWLDataFactory df = ontology.getOWLOntologyManager().
getOWLDataFactory();
OWLClass taxon = df.getOWLClass(iri);
assertTrue("Species class in signature",
ontology.containsClassInSignature(iri));
// Check axioms
Set<OWLClassAxiom> axioms = ontology.getAxioms(taxon, Imports.EXCLUDED);
assertEquals("Count class axioms", 1, axioms.size());
assertEquals("SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_species> <http://purl.obolibrary.org/obo/NCBITaxon#_taxonomic_rank>)", axioms.toArray()[0].toString());
// Check annotations
List<String> values = new ArrayList<String>();
values.add("AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_species> \"ncbi_taxonomy\"^^xsd:string)");
values.add("AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_species> \"species\"^^xsd:string)");
Set<OWLAnnotationAssertionAxiom> annotations =
ontology.getAnnotationAssertionAxioms(iri);
assertEquals("Count annotations for Species", 2, annotations.size());
checkAnnotations(annotations, values);
}
开发者ID:owlcollab,项目名称:owltools,代码行数:25,代码来源:NCBI2OWLTest.java
示例3: processAnatomy
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
public void processAnatomy(Owlbuilder builder, OWLClass anatomyClass) {
final OWLOntologyManager manager = builder.getOntologyManager();
final OWLOntology merged = builder.getMergedSources();
final OWLOntology extracted = builder.getTarget();
if (true){
log.info("Need to add anatomy: " + anatomyClass.getIRI());
Set<OWLClassAxiom> anatAxioms = merged.getAxioms(anatomyClass,org.semanticweb.owlapi.model.parameters.Imports.INCLUDED);
manager.addAxioms(extracted, anatAxioms);
Set<OWLAnnotationAssertionAxiom> anatAnnotations =
merged.getAnnotationAssertionAxioms(anatomyClass.getIRI());
for (OWLAnnotationAssertionAxiom a : anatAnnotations){
//log.info(" Annotation Axiom: " + a.toString());
if (a.getAnnotation().getProperty().isLabel()){
log.info("Label is " + a.getAnnotation().getValue().toString());
manager.addAxiom(extracted, a);
}
}
}
builder.initializeMiscTermAndParents(anatomyClass);
}
开发者ID:pmidford,项目名称:owlbuilder,代码行数:22,代码来源:Participant.java
示例4: check
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
protected void check(OWLClass owlClass, OWLGraphWrapper graph, List<CheckWarning> warnings, OWLPrettyPrinter pp) {
final Set<OWLOntology> allOntologies = graph.getAllOntologies();
for(OWLOntology ontology : allOntologies){
Set<OWLClassAxiom> axioms = ontology.getAxioms(owlClass, Imports.EXCLUDED);
if (axioms != null && !axioms.isEmpty()) {
// check axioms
for (OWLClassAxiom axiom : axioms) {
Set<OWLClass> signature = axiom.getClassesInSignature();
for (OWLClass signatureClass : signature) {
if (graph.isObsolete(signatureClass)) {
StringBuilder sb = new StringBuilder();
sb.append("Obsolete class ");
String id = graph.getIdentifier(signatureClass);
if (id != null) {
sb.append(id);
String sigLabel = graph.getLabel(signatureClass);
if (sigLabel != null) {
sb.append(" '").append(sigLabel).append('\'');
}
}
else {
sb.append(signatureClass.getIRI());
}
sb.append(" in axiom: ");
sb.append(pp.render(axiom));
warnings.add(new CheckWarning(getID(), sb.toString() , isFatal(), owlClass.getIRI()));
}
}
}
}
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:33,代码来源:ObsoleteClassInSignature.java
示例5: check
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
protected void check(OWLClass owlClass, OWLGraphWrapper graph, Map<String, OWLObject> altIds, List<CheckWarning> warnings, OWLPrettyPrinter pp) {
final Set<OWLOntology> allOntologies = graph.getAllOntologies();
for(OWLOntology ontology : allOntologies){
Set<OWLClassAxiom> axioms = ontology.getAxioms(owlClass, Imports.EXCLUDED);
if (axioms != null && !axioms.isEmpty()) {
// check axioms
for (OWLClassAxiom axiom : axioms) {
Set<OWLClass> signature = axiom.getClassesInSignature();
for (OWLClass signatureClass : signature) {
String identifier = graph.getIdentifier(signatureClass);
if (identifier != null) {
OWLObject replacement = altIds.get(identifier);
if (replacement != null) {
StringBuilder sb = new StringBuilder();
sb.append("Alternate Identifier ");
sb.append(identifier);
sb.append(" for main class ");
String replacementId = graph.getIdentifier(replacement);
if (replacementId != null) {
sb.append(replacementId);
String replacementLabel = graph.getLabel(replacement);
if (replacementLabel != null) {
sb.append(" '").append(replacementLabel).append('\'');
}
}
else {
sb.append(replacement);
}
sb.append(" in axiom: ");
sb.append(pp.render(axiom));
warnings.add(new CheckWarning(getID(), sb.toString() , isFatal(), owlClass.getIRI()));
}
}
}
}
}
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:39,代码来源:AltIdInSignature.java
示例6: testBacteria
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
private void testBacteria(OWLOntology ontology) {
String curie = "ncbi:2";
IRI iri = OWLConverter.format.getIRI(curie);
OWLDataFactory df = ontology.getOWLOntologyManager().
getOWLDataFactory();
OWLClass taxon = df.getOWLClass(iri);
assertTrue("Bacteria class in signature",
ontology.containsClassInSignature(iri));
// Check axioms
Set<OWLClassAxiom> axioms = ontology.getAxioms(taxon, Imports.EXCLUDED);
assertEquals("Count class axioms for Bacteria", 1, axioms.size());
assertEquals("SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_2> <http://purl.obolibrary.org/obo/NCBITaxon_131567>)", axioms.toArray()[0].toString());
// Check annotations
List<String> values = new ArrayList<String>();
values.add(expandAnnotation(curie, "ncbitaxon:has_rank", OWLConverter.format.getIRI("ncbi:superkingdom")));
values.add(expandAnnotation(curie, "oio:hasOBONamespace", "ncbi_taxonomy"));
values.add(expandAnnotation(curie, "oio:hasDbXref", "GC_ID:11"));
values.add(expandLabel(curie, "rdfs:label", "Bacteria"));
values.add(expandSynonym(curie, "ncbitaxon:genbank_common_name", "oio:hasExactSynonym", "eubacteria"));
values.add(expandSynonym(curie, "ncbitaxon:synonym", "oio:hasRelatedSynonym", "not Bacteria Haeckel 1894"));
values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Prokaryota"));
values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Monera"));
values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Procaryotae"));
values.add(expandSynonym(curie, "ncbitaxon:in_part", "oio:hasRelatedSynonym", "Prokaryotae"));
values.add(expandSynonym(curie, "ncbitaxon:blast_name", "oio:hasRelatedSynonym", "eubacteria"));
Set<OWLAnnotationAssertionAxiom> annotations =
ontology.getAnnotationAssertionAxioms(iri);
assertEquals("Count annotations for Bacteria", values.size(), annotations.size());
checkAnnotations(annotations, values);
}
开发者ID:owlcollab,项目名称:owltools,代码行数:35,代码来源:NCBI2OWLTest.java
示例7: testActinobacteria
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
private void testActinobacteria(OWLOntology ontology) {
String curie = "ncbi:201174";
IRI iri = OWLConverter.format.getIRI(curie);
OWLDataFactory df = ontology.getOWLOntologyManager().
getOWLDataFactory();
OWLClass taxon = df.getOWLClass(iri);
assertTrue("Actinobacteria class in signature",
ontology.containsClassInSignature(iri));
// Check axioms
Set<OWLClassAxiom> axioms = ontology.getAxioms(taxon, Imports.EXCLUDED);
assertEquals("Count class axioms for Actinobacteria", 1, axioms.size());
assertEquals("SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_201174> <http://purl.obolibrary.org/obo/NCBITaxon_2>)", axioms.toArray()[0].toString());
// Check annotations
List<String> values = new ArrayList<String>();
values.add(expandAnnotation(curie, "ncbitaxon:has_rank", OWLConverter.format.getIRI("ncbi:phylum")));
values.add(expandAnnotation(curie, "oio:hasOBONamespace", "ncbi_taxonomy"));
values.add(expandAnnotation(curie, "oio:hasDbXref", "GC_ID:11"));
values.add(expandLabel(curie, "rdfs:label", "Actinobacteria [NCBITaxon:201174]"));
values.add(expandSynonym(curie, "ncbitaxon:scientific_name", "oio:hasExactSynonym", "Actinobacteria"));
values.add(expandSynonym(curie, "ncbitaxon:synonym", "oio:hasRelatedSynonym", "'Actinobacteria'"));
values.add(expandSynonym(curie, "ncbitaxon:synonym", "oio:hasRelatedSynonym", "not Actinobacteria Cavalier-Smith 2002"));
values.add(expandSynonym(curie, "ncbitaxon:blast_name", "oio:hasRelatedSynonym", "actinobacteria"));
Set<OWLAnnotationAssertionAxiom> annotations =
ontology.getAnnotationAssertionAxioms(iri);
assertEquals("Count annotations for Actinobacteria",
values.size(), annotations.size());
checkAnnotations(annotations, values);
}
开发者ID:owlcollab,项目名称:owltools,代码行数:33,代码来源:NCBI2OWLTest.java
示例8: fullEquivalenceClassesAreAdded
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
@Test
public void fullEquivalenceClassesAreAdded() throws Exception {
OWLClass e0 = dataFactory.getOWLClass(IRI.create("http://example.org/e0"));
OWLClass e1 = dataFactory.getOWLClass(IRI.create("http://example.org/e1"));
OWLClass e2 = dataFactory.getOWLClass(IRI.create("http://example.org/e2"));
OWLClassAxiom fullEquivalence = dataFactory.getOWLEquivalentClassesAxiom(e0, e1, e2);
assertThat(ont.containsAxiom(fullEquivalence), is(false));
util.removeUnsatisfiableClasses();
util.reason();
assertThat(ont.containsAxiom(fullEquivalence), is(true));
}
开发者ID:SciGraph,项目名称:SciGraph,代码行数:12,代码来源:ReasonerUtilTest.java
示例9: subclassHierarchyIsRepaired
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
@Test
public void subclassHierarchyIsRepaired() throws Exception {
OWLClass dx = dataFactory.getOWLClass(IRI.create("http://example.org/dx"));
OWLClass cx = dataFactory.getOWLClass(IRI.create("http://example.org/cx"));
OWLClass root = dataFactory.getOWLClass(IRI.create("http://example.org/root"));
OWLClassAxiom inferrredSubclass = dataFactory.getOWLSubClassOfAxiom(dx, cx);
OWLClassAxiom originalSubclass = dataFactory.getOWLSubClassOfAxiom(dx, root);
assertThat(ont.containsAxiom(inferrredSubclass), is(false));
assertThat(ont.containsAxiom(originalSubclass), is(true));
util.removeUnsatisfiableClasses();
util.reason();
assertThat(ont.containsAxiom(inferrredSubclass), is(true));
assertThat(ont.containsAxiom(originalSubclass), is(false));
}
开发者ID:SciGraph,项目名称:SciGraph,代码行数:15,代码来源:ReasonerUtilTest.java
示例10: redundantAxioms_areRemoved
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
@Test
public void redundantAxioms_areRemoved() throws Exception {
OWLClass e = dataFactory.getOWLClass(IRI.create("http://example.org/e"));
OWLClass c = dataFactory.getOWLClass(IRI.create("http://example.org/c"));
OWLClassAxiom originalSubclass = dataFactory.getOWLSubClassOfAxiom(e, c);
assertThat(ont.containsAxiom(originalSubclass), is(true));
util.removeRedundantAxioms();
assertThat(ont.containsAxiom(originalSubclass), is(false));
}
开发者ID:SciGraph,项目名称:SciGraph,代码行数:10,代码来源:ReasonerUtilTest.java
示例11: convert
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
@SuppressWarnings("static-method")
public ElkClassAxiom convert(OWLClassAxiom owlClassAxiom) {
return owlClassAxiom.accept(OWL_CLASS_AXIOM_CONVERTER);
}
开发者ID:liveontologies,项目名称:elk-reasoner,代码行数:5,代码来源:OwlConverter.java
示例12: assertAllInferences
import org.semanticweb.owlapi.model.OWLClassAxiom; //导入依赖的package包/类
public static void assertAllInferences(OWLGraphWrapper graph, String idsInputFile) {
final OWLOntology ontology = graph.getSourceOntology();
final OWLOntologyManager manager = ontology.getOWLOntologyManager();
final OWLDataFactory factory = manager.getOWLDataFactory();
Set<String> ids = loadIdsInputFile(idsInputFile);
final OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
final OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
try {
logger.info("Start check all");
// check all classes from the main ontology
AllInferenceReport report = new AllInferenceReport();
Set<OWLClass> classes = ontology.getClassesInSignature(Imports.EXCLUDED);
int count = 0;
int total = ids != null ? ids.size() : classes.size();
int step = 100;
for (final OWLClass owlClass : classes) {
if (ids != null) {
String id = graph.getIdentifier(owlClass);
if (ids.contains(id) == false) {
continue;
}
}
count += 1;
// get axioms for the current class
Set<OWLClassAxiom> axioms = ontology.getAxioms(owlClass, Imports.EXCLUDED);
handleAxioms(owlClass, axioms, ontology, manager, factory, reasoner, report);
// handleAxioms2(owlClass, axioms, ontology, manager, factory, reasoner, report);
if (count % step == 0) {
logger.info("Current count "+count+" of "+total);
}
}
PrintWriter writer = new PrintWriter(System.out);
report.printReport(writer);
writer.close();
}
finally {
reasoner.dispose();
}
}
开发者ID:owlcollab,项目名称:owltools,代码行数:43,代码来源:AssertInferenceTool.java
注:本文中的org.semanticweb.owlapi.model.OWLClassAxiom类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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