public class PhenoSimHQEPreProcessor extends AbstractOBOSimPreProcessor
Modifier and Type | Field and Description |
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protected String |
ABNORMAL |
protected boolean |
isMultiSpecies |
protected String |
QUALITY |
COMPOSED_PRIMARILY_OF, DEPENDS_ON, DEVELOPS_FROM, EXPRESSED_IN, HAS_PART, HAS_PHENOTYPE, INHERES_IN, INHERES_IN_PART_OF, PART_OF, QUALIFIER, RESULTS_IN_DEVELOPMENT_OF, RESULTS_IN_MORPHOGENESIS_OF
defaultLCSElementFrequencyThreshold, defaultNewIntersectionSimJThreshold, lcsCache
classesToSkip, LOG, materializedClassExpressionMap, saveIntermediateStates, simProperties
Constructor and Description |
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PhenoSimHQEPreProcessor() |
Modifier and Type | Method and Description |
---|---|
Set<org.semanticweb.owlapi.model.OWLClass> |
filterByDirectProperty(Set<org.semanticweb.owlapi.model.OWLClass> inSet,
org.semanticweb.owlapi.model.OWLObjectProperty p)
Note: if the ontology contains
Z SubClassOf df some Z2, Z2 SubClassOf U
then Z2 will be retained, but U will not.
|
protected Set<org.semanticweb.owlapi.model.OWLClass> |
getPhenotypeEntityClasses() |
Set<org.semanticweb.owlapi.model.OWLClass> |
getQualityClasses() |
boolean |
isVerbotenEntity(org.semanticweb.owlapi.model.OWLClass c) |
protected void |
makeDevelopmentMorphologyLinks()
In MP we have
+ abn.
|
protected void |
makeHasPhenotypeInstancesDirect() |
void |
preprocess()
Generate output ontology
|
addPropertyChain, getIRIViaOBOSuffix, getOWLClassViaOBOSuffix, getOWLObjectPropertyViaOBOSuffix, makePartOfReflexive, makeReflexive
generateLeastCommonSubsumers, generateLeastCommonSubsumersForAttributeClasses, getLowestCommonSubsumer, getLowestCommonSubsumer, getLowestCommonSubsumerClass, getNamedCommonSubsumers, getNamedCommonSubsumers, getNamedLowestCommonSubsumers, getNamedReflexiveSubsumers, getNamedSubsumers, getNamedSubsumers, makeClass
addAxiomsToOutput, addAxiomToOutput, addViewMapping, assertInferredForAttributeClasses, createPropertyView, createPropertyView, createPropertyView, createPropertyView, dispose, extractClassesFromDeclarations, filterUnused, flush, generateLabel, getAboxProperty, getAnyLabel, getAttributeClasses, getDirectAttributeClassExpressions, getInputOntology, getLabel, getOutputOntology, getProperty, getReasoner, getReflexiveSubClasses, getSimProperties, getViewClasses, ignoreClasses, isUpperLevel, makeReflexive, makeReflexive, makeViewClassIRI, makeViewClassIRI, materializeClassExpression, materializeClassExpressions, materializeClassExpressionsReferencedBy, MD5, removeAxiomsFromOutput, removeDisjointClassesAxioms, removeUnreachableAxioms, saveState, setInputOntology, setOutputOntology, setOWLPrettyPrinter, setReasoner, setReasonerFactory, setSimProperties, trim
protected String QUALITY
protected String ABNORMAL
protected boolean isMultiSpecies
public void preprocess()
SimPreProcessor
preprocess
in interface SimPreProcessor
preprocess
in class AbstractSimPreProcessor
protected void makeHasPhenotypeInstancesDirect()
protected void makeDevelopmentMorphologyLinks()
protected Set<org.semanticweb.owlapi.model.OWLClass> getPhenotypeEntityClasses()
public boolean isVerbotenEntity(org.semanticweb.owlapi.model.OWLClass c)
public Set<org.semanticweb.owlapi.model.OWLClass> getQualityClasses()
public Set<org.semanticweb.owlapi.model.OWLClass> filterByDirectProperty(Set<org.semanticweb.owlapi.model.OWLClass> inSet, org.semanticweb.owlapi.model.OWLObjectProperty p)
inSet
- p
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