org.obolibrary.obo2owl
Class Owl2Obo

java.lang.Object
  extended by org.obolibrary.obo2owl.Owl2Obo

public class Owl2Obo
extends Object


Nested Class Summary
static class Owl2Obo.UntranslatableAxiomException
           
 
Field Summary
static Map<String,String> annotationPropertyMap
           
 
Constructor Summary
Owl2Obo()
           
 
Method Summary
 OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ont)
           
static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
          See table 5.9.2.
 String getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)
           
static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.OWLOntology ont)
          Retrieve the identifier for a given OWLObject.
static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj, org.semanticweb.owlapi.model.OWLOntology ont, String defaultValue)
          Retrieve the identifier for a given OWLObject.
 org.semanticweb.owlapi.model.OWLOntologyManager getManager()
           
 OBODoc getObodoc()
           
static String getOntologyId(org.semanticweb.owlapi.model.IRI iriObj)
           
static String getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology)
          E.g.
 boolean getStrictConversion()
           
 Collection<org.semanticweb.owlapi.model.OWLAxiom> getUntranslatableAxioms()
           
static String owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)
           
 void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
           
 void setObodoc(OBODoc obodoc)
           
 void setStrictConversion(boolean b)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

annotationPropertyMap

public static Map<String,String> annotationPropertyMap
Constructor Detail

Owl2Obo

public Owl2Obo()
Method Detail

setStrictConversion

public void setStrictConversion(boolean b)

getStrictConversion

public boolean getStrictConversion()

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)

convert

public OBODoc convert(org.semanticweb.owlapi.model.OWLOntology ont)
               throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

getUntranslatableAxioms

public Collection<org.semanticweb.owlapi.model.OWLAxiom> getUntranslatableAxioms()
Returns:
the untranslatableAxioms

getOntologyId

public static String getOntologyId(org.semanticweb.owlapi.model.OWLOntology ontology)
E.g. http://purl.obolibrary.org/obo/go.owl --> "go" if does not match this pattern, then retain original IRI

Parameters:
ontology -
Returns:
The OBO ID of the ontology

getOntologyId

public static String getOntologyId(org.semanticweb.owlapi.model.IRI iriObj)

getIdentifier

public String getIdentifier(org.semanticweb.owlapi.model.OWLObject obj)

getIdentifierFromObject

public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
                                             org.semanticweb.owlapi.model.OWLOntology ont,
                                             String defaultValue)
Retrieve the identifier for a given OWLObject. This methods uses also shorthand hints to resolve the identifier. Should the translation process encounter a problem or not find an identifier the defaultValue is returned.

Parameters:
obj - the OWLObject to resolve
ont - the target ontology
defaultValue - the value to return in case of an error or no id
Returns:
identifier or the default value

getIdentifierFromObject

public static String getIdentifierFromObject(org.semanticweb.owlapi.model.OWLObject obj,
                                             org.semanticweb.owlapi.model.OWLOntology ont)
                                      throws Owl2Obo.UntranslatableAxiomException
Retrieve the identifier for a given OWLObject. This methods uses also shorthand hints to resolve the identifier. Should the translation process encounter an unexpected axiom an Owl2Obo.UntranslatableAxiomException is thrown.

Parameters:
obj - the OWLObject to resolve
ont - the target ontology
Returns:
identifier or null
Throws:
Owl2Obo.UntranslatableAxiomException

getIdentifier

public static String getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
See table 5.9.2. Translation of identifiers

Parameters:
iriId -
Returns:
obo identifier or null

owlObjectToTag

public static String owlObjectToTag(org.semanticweb.owlapi.model.OWLObject obj)


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