public class OldSimpleOwlSim extends Object
ABox: a collection of individuals to be compared, plus class assertions TBox: actual ontology
Optionally: a list of "SEP" properties, plus a list of classification properties.
E.g. Individual: organism1 Types: human, has_phenotype some HP_nnnnn
After this has completed, standard semantc similarity measures are applied.
These steps can be decoupled.
For example, if P is part_of, and O contains an anatomy ontology, then the resulting hierarchy will be a snomed-like: hepatocyte SubClassOf cell, liver part etc.
Thus if E = has_phenotype, and C = lung, if there are no elements that instantiate has_phenotype some lung. this is rejected.
Modifier and Type | Class and Description |
---|---|
static class |
OldSimpleOwlSim.EnrichmentConfig |
class |
OldSimpleOwlSim.EnrichmentResult |
class |
OldSimpleOwlSim.OWLClassExpressionPair |
class |
OldSimpleOwlSim.ScoreAttributePair |
class |
OldSimpleOwlSim.ScoreAttributesPair |
static class |
OldSimpleOwlSim.Stage |
Modifier and Type | Field and Description |
---|---|
String |
baseFileName |
OldSimpleOwlSim.EnrichmentConfig |
enrichmentConfig |
OWLPrettyPrinter |
owlpp |
Constructor and Description |
---|
OldSimpleOwlSim(org.semanticweb.owlapi.model.OWLOntology sourceOntology) |
Modifier and Type | Method and Description |
---|---|
void |
addIgnoreSubClassesOf(org.semanticweb.owlapi.model.IRI iri) |
void |
addIgnoreSubClassesOf(org.semanticweb.owlapi.model.OWLClass c) |
void |
addSourceViewProperty(org.semanticweb.owlapi.model.IRI iri) |
void |
addSourceViewProperty(org.semanticweb.owlapi.model.OWLObjectProperty p)
Deprecated.
|
void |
addViewProperty(org.semanticweb.owlapi.model.IRI iri)
Deprecated.
|
void |
addViewProperty(org.semanticweb.owlapi.model.OWLObjectProperty viewProperty)
Deprecated.
|
void |
assertInferences(boolean isRemoveLogicalAxioms) |
List<OldSimpleOwlSim.EnrichmentResult> |
calculateAllByAllEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass,
org.semanticweb.owlapi.model.OWLClass pc1,
org.semanticweb.owlapi.model.OWLClass pc2) |
List<OldSimpleOwlSim.EnrichmentResult> |
calculateEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass,
org.semanticweb.owlapi.model.OWLClass sampleSetClass) |
OldSimpleOwlSim.EnrichmentResult |
calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass,
org.semanticweb.owlapi.model.OWLClass sampleSetClass,
org.semanticweb.owlapi.model.OWLClass enrichedClass) |
void |
createElementAttributeMapFromOntology()
assumes that the ontology contains both attributes (TBox) and elements + associations (ABox)
|
void |
generateGroupingClasses()
Deprecated.
|
void |
generatePropertyViews()
Deprecated.
|
void |
generateSourcePropertyViews()
Deprecated.
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getAllAttributeClasses()
returns all attribute classes - i.e.
|
void |
getAllByAllLowestCommonSubsumer()
Deprecated.
|
Set<org.semanticweb.owlapi.model.OWLEntity> |
getAllElements() |
float |
getAttributeJaccardSimilarity(org.semanticweb.owlapi.model.OWLClassExpression a,
org.semanticweb.owlapi.model.OWLClassExpression b) |
Set<org.semanticweb.owlapi.model.OWLClass> |
getAttributesForElement(org.semanticweb.owlapi.model.OWLEntity e) |
String |
getBaseFileName() |
int |
getCorpusSize() |
float |
getElementJaccardSimilarity(org.semanticweb.owlapi.model.OWLNamedIndividual a,
org.semanticweb.owlapi.model.OWLNamedIndividual b) |
Set<org.semanticweb.owlapi.model.OWLEntity> |
getElementsForAttribute(org.semanticweb.owlapi.model.OWLClass c)
inferred
|
OldSimpleOwlSim.EnrichmentConfig |
getEnrichmentConfig() |
Set<org.semanticweb.owlapi.model.OWLClass> |
getIgnoreSubClassesOf() |
Double |
getInformationContentForAttribute(org.semanticweb.owlapi.model.OWLClass c) |
org.semanticweb.owlapi.model.OWLClassExpression |
getLowestCommonSubsumer(org.semanticweb.owlapi.model.OWLClassExpression a,
org.semanticweb.owlapi.model.OWLClassExpression b)
gets the LCS.
|
org.semanticweb.owlapi.model.OWLClass |
getLowestCommonSubsumerClass(org.semanticweb.owlapi.model.OWLClassExpression a,
org.semanticweb.owlapi.model.OWLClassExpression b)
generates a LCS expression and makes it a class if it is a class expression
|
OldSimpleOwlSim.ScoreAttributePair |
getLowestCommonSubsumerIC(org.semanticweb.owlapi.model.OWLClassExpression a,
org.semanticweb.owlapi.model.OWLClassExpression b) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedCommonSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a,
org.semanticweb.owlapi.model.OWLClassExpression b) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedCommonSubsumers(org.semanticweb.owlapi.model.OWLNamedIndividual a,
org.semanticweb.owlapi.model.OWLNamedIndividual b) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedLowestCommonSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a,
org.semanticweb.owlapi.model.OWLClassExpression b) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedReflexiveSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a) |
Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> |
getNamedSubsumers(org.semanticweb.owlapi.model.OWLNamedIndividual a) |
int |
getNumElementsForAttribute(org.semanticweb.owlapi.model.OWLClass c)
|{e|e in a(c)}|
|
org.semanticweb.owlapi.reasoner.OWLReasoner |
getReasoner() |
org.semanticweb.owlapi.reasoner.OWLReasonerFactory |
getReasonerFactory() |
OldSimpleOwlSim.ScoreAttributesPair |
getSimilarityBestMatchAverageAsym(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j)
Pesquita et al
|
OldSimpleOwlSim.ScoreAttributesPair |
getSimilarityMaxIC(org.semanticweb.owlapi.model.OWLNamedIndividual i,
org.semanticweb.owlapi.model.OWLNamedIndividual j) |
SimPreProcessor |
getSimPreProcessor() |
List<org.semanticweb.owlapi.model.OWLObjectProperty> |
getSourceViewProperties()
Deprecated.
|
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
getViewProperties() |
void |
makeAllByAllLowestCommonSubsumer() |
org.semanticweb.owlapi.model.OWLClass |
makeClass(org.semanticweb.owlapi.model.OWLObjectIntersectionOf x)
given a CE of the form A1 and A2 and ...
|
void |
precomputeAttributeElementCount() |
void |
preprocess()
NEW:
externalize preprocessing to separate class
|
void |
reason() |
void |
removeUnreachableAxioms()
If a node cannot be reached on the existential graph, then remove it.
|
void |
saveOntology(OldSimpleOwlSim.Stage stage) |
void |
saveOntology(String fn) |
void |
setAttributesFromOntology(org.semanticweb.owlapi.model.OWLOntology o)
Deprecated.
|
void |
setBaseFileName(String baseFileName) |
void |
setCorpusSize(int size) |
void |
setEnrichmentConfig(OldSimpleOwlSim.EnrichmentConfig enrichmentConfig) |
void |
setIgnoreSubClassesOf(Set<org.semanticweb.owlapi.model.OWLClass> ignoreSubClassesOf) |
void |
setReasoner(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner) |
void |
setReasonerFactory(org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory) |
void |
setSimPreProcessor(SimPreProcessor simPreProcessor) |
void |
setSourceViewProperties(List<org.semanticweb.owlapi.model.OWLObjectProperty> sourceViewProperties)
Deprecated.
|
void |
setViewProperties(Set<org.semanticweb.owlapi.model.OWLObjectProperty> viewProperties)
Deprecated.
|
public OWLPrettyPrinter owlpp
public String baseFileName
public OldSimpleOwlSim.EnrichmentConfig enrichmentConfig
public OldSimpleOwlSim(org.semanticweb.owlapi.model.OWLOntology sourceOntology)
public org.semanticweb.owlapi.reasoner.OWLReasonerFactory getReasonerFactory()
public void setReasonerFactory(org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory)
public SimPreProcessor getSimPreProcessor()
public void setSimPreProcessor(SimPreProcessor simPreProcessor)
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> getViewProperties()
@Deprecated public void setViewProperties(Set<org.semanticweb.owlapi.model.OWLObjectProperty> viewProperties)
@Deprecated public void addViewProperty(org.semanticweb.owlapi.model.OWLObjectProperty viewProperty)
@Deprecated public void addViewProperty(org.semanticweb.owlapi.model.IRI iri)
@Deprecated public List<org.semanticweb.owlapi.model.OWLObjectProperty> getSourceViewProperties()
@Deprecated public void setSourceViewProperties(List<org.semanticweb.owlapi.model.OWLObjectProperty> sourceViewProperties)
@Deprecated public void addSourceViewProperty(org.semanticweb.owlapi.model.OWLObjectProperty p)
public void addSourceViewProperty(org.semanticweb.owlapi.model.IRI iri)
public Set<org.semanticweb.owlapi.model.OWLClass> getIgnoreSubClassesOf()
public void setIgnoreSubClassesOf(Set<org.semanticweb.owlapi.model.OWLClass> ignoreSubClassesOf)
public void addIgnoreSubClassesOf(org.semanticweb.owlapi.model.OWLClass c)
public void addIgnoreSubClassesOf(org.semanticweb.owlapi.model.IRI iri)
public String getBaseFileName()
public void setBaseFileName(String baseFileName)
public void preprocess()
@Deprecated public void generateGroupingClasses() throws org.semanticweb.owlapi.model.OWLOntologyCreationException, FileNotFoundException, org.semanticweb.owlapi.model.OWLOntologyStorageException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyStorageException
FileNotFoundException
@Deprecated public void generatePropertyViews() throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
@Deprecated public void generateSourcePropertyViews() throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void saveOntology(OldSimpleOwlSim.Stage stage) throws FileNotFoundException, org.semanticweb.owlapi.model.OWLOntologyStorageException
FileNotFoundException
org.semanticweb.owlapi.model.OWLOntologyStorageException
public void saveOntology(String fn) throws FileNotFoundException, org.semanticweb.owlapi.model.OWLOntologyStorageException
FileNotFoundException
org.semanticweb.owlapi.model.OWLOntologyStorageException
public org.semanticweb.owlapi.reasoner.OWLReasoner getReasoner()
public void setReasoner(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
public void reason()
public void removeUnreachableAxioms()
public void assertInferences(boolean isRemoveLogicalAxioms)
public void makeAllByAllLowestCommonSubsumer()
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a)
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedSubsumers(org.semanticweb.owlapi.model.OWLNamedIndividual a)
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedReflexiveSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a)
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedCommonSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a, org.semanticweb.owlapi.model.OWLClassExpression b)
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedCommonSubsumers(org.semanticweb.owlapi.model.OWLNamedIndividual a, org.semanticweb.owlapi.model.OWLNamedIndividual b)
public Set<org.semanticweb.owlapi.reasoner.Node<org.semanticweb.owlapi.model.OWLClass>> getNamedLowestCommonSubsumers(org.semanticweb.owlapi.model.OWLClassExpression a, org.semanticweb.owlapi.model.OWLClassExpression b)
public org.semanticweb.owlapi.model.OWLClassExpression getLowestCommonSubsumer(org.semanticweb.owlapi.model.OWLClassExpression a, org.semanticweb.owlapi.model.OWLClassExpression b)
a
- b
- public org.semanticweb.owlapi.model.OWLClass getLowestCommonSubsumerClass(org.semanticweb.owlapi.model.OWLClassExpression a, org.semanticweb.owlapi.model.OWLClassExpression b)
a
- b
- public float getAttributeJaccardSimilarity(org.semanticweb.owlapi.model.OWLClassExpression a, org.semanticweb.owlapi.model.OWLClassExpression b)
a
- b
- public float getElementJaccardSimilarity(org.semanticweb.owlapi.model.OWLNamedIndividual a, org.semanticweb.owlapi.model.OWLNamedIndividual b)
public OldSimpleOwlSim.ScoreAttributePair getLowestCommonSubsumerIC(org.semanticweb.owlapi.model.OWLClassExpression a, org.semanticweb.owlapi.model.OWLClassExpression b)
public OldSimpleOwlSim.ScoreAttributesPair getSimilarityMaxIC(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j)
public OldSimpleOwlSim.ScoreAttributesPair getSimilarityBestMatchAverageAsym(org.semanticweb.owlapi.model.OWLNamedIndividual i, org.semanticweb.owlapi.model.OWLNamedIndividual j)
i
- j
- public OldSimpleOwlSim.EnrichmentConfig getEnrichmentConfig()
public void setEnrichmentConfig(OldSimpleOwlSim.EnrichmentConfig enrichmentConfig)
public List<OldSimpleOwlSim.EnrichmentResult> calculateAllByAllEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass, org.semanticweb.owlapi.model.OWLClass pc1, org.semanticweb.owlapi.model.OWLClass pc2) throws org.apache.commons.math.MathException
populationClass
- pc1
- - sample set classpc2
- - enriched set classorg.apache.commons.math.MathException
public List<OldSimpleOwlSim.EnrichmentResult> calculateEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass, org.semanticweb.owlapi.model.OWLClass sampleSetClass) throws org.apache.commons.math.MathException
org.apache.commons.math.MathException
public OldSimpleOwlSim.EnrichmentResult calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass populationClass, org.semanticweb.owlapi.model.OWLClass sampleSetClass, org.semanticweb.owlapi.model.OWLClass enrichedClass) throws org.apache.commons.math.MathException
populationClass
- sampleSetClass
- enrichedClass
- org.apache.commons.math.MathException
public Set<org.semanticweb.owlapi.model.OWLClass> getAllAttributeClasses()
@Deprecated public void setAttributesFromOntology(org.semanticweb.owlapi.model.OWLOntology o)
public void createElementAttributeMapFromOntology()
public Set<org.semanticweb.owlapi.model.OWLClass> getAttributesForElement(org.semanticweb.owlapi.model.OWLEntity e)
public void precomputeAttributeElementCount()
public Set<org.semanticweb.owlapi.model.OWLEntity> getElementsForAttribute(org.semanticweb.owlapi.model.OWLClass c)
c
- public int getNumElementsForAttribute(org.semanticweb.owlapi.model.OWLClass c)
c
- public Set<org.semanticweb.owlapi.model.OWLEntity> getAllElements()
public int getCorpusSize()
public void setCorpusSize(int size)
public Double getInformationContentForAttribute(org.semanticweb.owlapi.model.OWLClass c)
@Deprecated public void getAllByAllLowestCommonSubsumer()
public org.semanticweb.owlapi.model.OWLClass makeClass(org.semanticweb.owlapi.model.OWLObjectIntersectionOf x)
x
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