owltools.gaf.owl
Class GAFOWLBridge

java.lang.Object
  extended by owltools.gaf.owl.GAFOWLBridge
Direct Known Subclasses:
AnnotationExtensionFolder, AnnotationExtensionUnfolder, BasicABox

public class GAFOWLBridge
extends Object


Nested Class Summary
static class GAFOWLBridge.BioentityMapping
           
 class GAFOWLBridge.GAFDescription
           
static class GAFOWLBridge.Vocab
           
 
Field Summary
static org.semanticweb.owlapi.model.IRI GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI
           
protected  OWLGraphWrapper graph
           
 
Constructor Summary
GAFOWLBridge(OWLGraphWrapper g)
           
GAFOWLBridge(OWLGraphWrapper g, org.semanticweb.owlapi.model.OWLOntology tgtOnt)
          The ontology generated from the gaf will be placed in tgtOnt The graphwrapper object should include ontologies required to resolve certain entities, including the relations used in col16.
 
Method Summary
protected  void addAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms)
           
 GAFOWLBridge.BioentityMapping getBioentityMapping()
           
protected  List<GAFOWLBridge.GAFDescription> getDescription(GeneAnnotation a)
           
protected  org.semanticweb.owlapi.model.OWLObjectProperty getObjectPropertyByShorthand(String id)
           
protected  org.semanticweb.owlapi.model.OWLClass getOWLClass(String id)
           
 org.semanticweb.owlapi.model.OWLOntology getTargetOntology()
           
 boolean isBasicAboxMapping()
           
 boolean isGenerateIndividuals()
           
 void setBasicAboxMapping(boolean isBasicAboxMapping)
           
 void setBioentityMapping(GAFOWLBridge.BioentityMapping bioentityMapping)
           
 void setGenerateIndividuals(boolean isGenerateIndividuals)
           
 void setTargetOntology(org.semanticweb.owlapi.model.OWLOntology targetOntology)
           
 org.semanticweb.owlapi.model.OWLOntology translate(GafDocument gafdoc)
           
protected  void translateBioentity(Bioentity e)
           
 void translateGeneAnnotation(GeneAnnotation a)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

graph

protected OWLGraphWrapper graph

GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI

public static org.semanticweb.owlapi.model.IRI GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI
Constructor Detail

GAFOWLBridge

public GAFOWLBridge(OWLGraphWrapper g)

GAFOWLBridge

public GAFOWLBridge(OWLGraphWrapper g,
                    org.semanticweb.owlapi.model.OWLOntology tgtOnt)
The ontology generated from the gaf will be placed in tgtOnt The graphwrapper object should include ontologies required to resolve certain entities, including the relations used in col16. In future it will also be used to translate GAF evidence codes into ECO class IRIs. These ontologies could be the main ontology or support ontologies. A standard pattern is to have GO as the main, ro.owl and go/extensions/gorel.owl as support. (gorel is where many of the c16 relations are declared)

Parameters:
g -
tgtOnt -
Method Detail

getBioentityMapping

public GAFOWLBridge.BioentityMapping getBioentityMapping()
Returns:
the bioentityMapping

setBioentityMapping

public void setBioentityMapping(GAFOWLBridge.BioentityMapping bioentityMapping)
Parameters:
bioentityMapping - the bioentityMapping to set

isGenerateIndividuals

public boolean isGenerateIndividuals()

setGenerateIndividuals

public void setGenerateIndividuals(boolean isGenerateIndividuals)

isBasicAboxMapping

public boolean isBasicAboxMapping()

setBasicAboxMapping

public void setBasicAboxMapping(boolean isBasicAboxMapping)

getTargetOntology

public org.semanticweb.owlapi.model.OWLOntology getTargetOntology()

setTargetOntology

public void setTargetOntology(org.semanticweb.owlapi.model.OWLOntology targetOntology)

translate

public org.semanticweb.owlapi.model.OWLOntology translate(GafDocument gafdoc)
Parameters:
gafdoc -
Returns:
translated ontology

getDescription

protected List<GAFOWLBridge.GAFDescription> getDescription(GeneAnnotation a)

translateGeneAnnotation

public void translateGeneAnnotation(GeneAnnotation a)

getObjectPropertyByShorthand

protected org.semanticweb.owlapi.model.OWLObjectProperty getObjectPropertyByShorthand(String id)

getOWLClass

protected org.semanticweb.owlapi.model.OWLClass getOWLClass(String id)

translateBioentity

protected void translateBioentity(Bioentity e)

addAxioms

protected void addAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms)


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