public class GAFOWLBridge extends Object
Modifier and Type | Class and Description |
---|---|
static class |
GAFOWLBridge.BioentityMapping |
class |
GAFOWLBridge.GAFDescription |
static class |
GAFOWLBridge.Vocab |
Modifier and Type | Field and Description |
---|---|
static org.semanticweb.owlapi.model.IRI |
GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI |
protected OWLGraphWrapper |
graph |
Constructor and Description |
---|
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.
|
Modifier and Type | Method and Description |
---|---|
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() |
boolean |
isSkipNotAnnotations() |
void |
setBasicAboxMapping(boolean isBasicAboxMapping) |
void |
setBioentityMapping(GAFOWLBridge.BioentityMapping bioentityMapping) |
void |
setGenerateIndividuals(boolean isGenerateIndividuals) |
void |
setSkipNotAnnotations(boolean isSkipNotAnnotations) |
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) |
protected OWLGraphWrapper graph
public static org.semanticweb.owlapi.model.IRI GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI
public GAFOWLBridge(OWLGraphWrapper g)
public GAFOWLBridge(OWLGraphWrapper g, org.semanticweb.owlapi.model.OWLOntology tgtOnt)
g
- tgtOnt
- public GAFOWLBridge.BioentityMapping getBioentityMapping()
public void setBioentityMapping(GAFOWLBridge.BioentityMapping bioentityMapping)
bioentityMapping
- the bioentityMapping to setpublic boolean isGenerateIndividuals()
public void setGenerateIndividuals(boolean isGenerateIndividuals)
public boolean isBasicAboxMapping()
public void setBasicAboxMapping(boolean isBasicAboxMapping)
public org.semanticweb.owlapi.model.OWLOntology getTargetOntology()
public void setTargetOntology(org.semanticweb.owlapi.model.OWLOntology targetOntology)
public boolean isSkipNotAnnotations()
public void setSkipNotAnnotations(boolean isSkipNotAnnotations)
public org.semanticweb.owlapi.model.OWLOntology translate(GafDocument gafdoc)
gafdoc
- protected List<GAFOWLBridge.GAFDescription> getDescription(GeneAnnotation a)
public void translateGeneAnnotation(GeneAnnotation a)
protected org.semanticweb.owlapi.model.OWLObjectProperty getObjectPropertyByShorthand(String id)
protected org.semanticweb.owlapi.model.OWLClass getOWLClass(String id)
protected void translateBioentity(Bioentity e)
protected void addAxioms(Set<org.semanticweb.owlapi.model.OWLAxiom> axioms)
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