org.obolibrary.obo2owl
Class Obo2Owl
java.lang.Object
org.obolibrary.obo2owl.Obo2Owl
- Direct Known Subclasses:
- Obo2OWLOldMapping
public class Obo2Owl
- extends Object
Constructor Summary |
Obo2Owl()
|
Obo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DEBUG
public static final boolean DEBUG
DEFAULT_IRI_PREFIX
@Deprecated
public static final String DEFAULT_IRI_PREFIX
- Deprecated.
- Use conversion methods or Obo2OWLConstants.DEFAULT_IRI_PREFIX
- See Also:
- Constant Field Values
IRI_PROP_isReversiblePropertyChain
public static final String IRI_PROP_isReversiblePropertyChain
- See Also:
- Constant Field Values
annotationPropertyMap
public static Map<String,org.semanticweb.owlapi.model.IRI> annotationPropertyMap
Obo2Owl
public Obo2Owl()
Obo2Owl
public Obo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)
convertURL
public static void convertURL(String iri,
String outFile)
throws IOException,
org.semanticweb.owlapi.model.OWLOntologyCreationException,
org.semanticweb.owlapi.model.OWLOntologyStorageException
- Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
convertURL
public static void convertURL(String iri,
String outFile,
String defaultOnt)
throws IOException,
org.semanticweb.owlapi.model.OWLOntologyCreationException,
org.semanticweb.owlapi.model.OWLOntologyStorageException
- Parameters:
iri
- outFile
- defaultOnt
- -- e.g. "go". If the obo file contains no "ontology:" header tag, this is added
- Throws:
IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
getManager
public org.semanticweb.owlapi.model.OWLOntologyManager getManager()
setManager
public void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
getObodoc
public OBODoc getObodoc()
setObodoc
public void setObodoc(OBODoc obodoc)
getOwlOntology
protected org.semanticweb.owlapi.model.OWLOntology getOwlOntology()
- Returns:
- the owlOntology
setOwlOntology
protected void setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology)
- Parameters:
owlOntology
- the owlOntology to set
convert
public org.semanticweb.owlapi.model.OWLOntology convert(String oboFile)
throws org.semanticweb.owlapi.model.OWLOntologyCreationException
- Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
convert
public org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc)
throws org.semanticweb.owlapi.model.OWLOntologyCreationException
- Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
trHeaderFrame
public void trHeaderFrame(Frame headerFrame)
addOntologyAnnotation
protected void addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap,
org.semanticweb.owlapi.model.OWLAnnotationValue v)
trTermFrame
public org.semanticweb.owlapi.model.OWLClassExpression trTermFrame(Frame termFrame)
trTypedefFrame
public org.semanticweb.owlapi.model.OWLNamedObject trTypedefFrame(Frame typedefFrame)
add
protected void add(org.semanticweb.owlapi.model.OWLAxiom axiom)
apply
protected void apply(org.semanticweb.owlapi.model.OWLOntologyChange change)
trGenericClause
protected org.semanticweb.owlapi.model.OWLAxiom trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub,
String tag,
Clause clause)
trRel
public org.semanticweb.owlapi.model.OWLClassExpression trRel(String relId,
String classId,
Collection<QualifierValue> quals)
trTagToIRI
public static org.semanticweb.owlapi.model.IRI trTagToIRI(String tag)
trLiteral
protected org.semanticweb.owlapi.model.OWLAnnotationValue trLiteral(Object value)
oboIdToIRI
public org.semanticweb.owlapi.model.IRI oboIdToIRI(String id)
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