owltools.gaf.owl
Class GAFOWLBridge
java.lang.Object
owltools.gaf.owl.GAFOWLBridge
- Direct Known Subclasses:
- AnnotationExtensionFolder, AnnotationExtensionUnfolder, BasicABox
public class GAFOWLBridge
- extends Object
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. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
graph
protected OWLGraphWrapper graph
GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI
public static org.semanticweb.owlapi.model.IRI GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI
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
-
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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