org.obolibrary.obo2owl
Class Obo2Owl

java.lang.Object
  extended by org.obolibrary.obo2owl.Obo2Owl
Direct Known Subclasses:
Obo2OWLOldMapping

public class Obo2Owl
extends Object


Field Summary
static Map<String,org.semanticweb.owlapi.model.IRI> annotationPropertyMap
           
static boolean DEBUG
           
static String DEFAULT_IRI_PREFIX
          Deprecated. 
static String IRI_PROP_isReversiblePropertyChain
           
 
Constructor Summary
Obo2Owl()
           
Obo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)
           
 
Method Summary
protected  void add(org.semanticweb.owlapi.model.OWLAxiom axiom)
           
protected  void addOntologyAnnotation(org.semanticweb.owlapi.model.OWLAnnotationProperty ap, org.semanticweb.owlapi.model.OWLAnnotationValue v)
           
protected  void apply(org.semanticweb.owlapi.model.OWLOntologyChange change)
           
 org.semanticweb.owlapi.model.OWLOntology convert(OBODoc obodoc)
           
 org.semanticweb.owlapi.model.OWLOntology convert(String oboFile)
           
static void convertURL(String iri, String outFile)
           
static void convertURL(String iri, String outFile, String defaultOnt)
           
 org.semanticweb.owlapi.model.OWLOntologyManager getManager()
           
 OBODoc getObodoc()
           
protected  org.semanticweb.owlapi.model.OWLOntology getOwlOntology()
           
 org.semanticweb.owlapi.model.IRI oboIdToIRI(String id)
           
 void setManager(org.semanticweb.owlapi.model.OWLOntologyManager manager)
           
 void setObodoc(OBODoc obodoc)
           
protected  void setOwlOntology(org.semanticweb.owlapi.model.OWLOntology owlOntology)
           
protected  org.semanticweb.owlapi.model.OWLAxiom trGenericClause(org.semanticweb.owlapi.model.OWLAnnotationSubject sub, String tag, Clause clause)
           
 void trHeaderFrame(Frame headerFrame)
           
protected  org.semanticweb.owlapi.model.OWLAnnotationValue trLiteral(Object value)
           
 org.semanticweb.owlapi.model.OWLClassExpression trRel(String relId, String classId, Collection<QualifierValue> quals)
           
static org.semanticweb.owlapi.model.IRI trTagToIRI(String tag)
           
 org.semanticweb.owlapi.model.OWLClassExpression trTermFrame(Frame termFrame)
           
 org.semanticweb.owlapi.model.OWLNamedObject trTypedefFrame(Frame typedefFrame)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DEBUG

public static final boolean DEBUG

DEFAULT_IRI_PREFIX

@Deprecated
public static final String DEFAULT_IRI_PREFIX
Deprecated. 
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
Constructor Detail

Obo2Owl

public Obo2Owl()

Obo2Owl

public Obo2Owl(org.semanticweb.owlapi.model.OWLOntologyManager manager)
Method Detail

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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