public class LegoModelGenerator extends MinimalModelGenerator
#seedGraph
- seed initial A
#createPartonomy
- create partonomy P
connectGraph()
- created activity network E
https://docs.google.com/document/d/1TV8Eb9sSvFY-weVZaIfzCxF1qbnmkUaiUhTm9Bs3gRE/edit
Modifier and Type | Field and Description |
---|---|
Set<org.semanticweb.owlapi.model.OWLClass> |
processClassSet |
isStrict, model, prototypeIndividualMap
Constructor and Description |
---|
LegoModelGenerator(ModelContainer model) |
Modifier and Type | Method and Description |
---|---|
void |
addGenes(org.semanticweb.owlapi.model.OWLClass processCls) |
void |
addGenes(org.semanticweb.owlapi.model.OWLClass processCls,
Collection<String> seedGenes)
Create initial activation node set A for a process P and a set of seed genes
for all g ∈ Gseed, add a =
|
void |
addGenes(String processClsId,
Collection<String> seedGenes) |
void |
anonymizeMaterialEntities()
Example: if we have triples:
|
void |
buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls,
Collection<String> seedGenes)
Performs all steps to seed activation network.
|
void |
buildNetwork(String processClsId,
Collection<String> seedGenes)
|
Double |
calculateConditionalProbaility(org.semanticweb.owlapi.model.OWLClass wholeCls,
org.semanticweb.owlapi.model.OWLClass partCls)
Pr( F | P ) = Pr(F,P) / Pr(P)
|
Double |
calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass sampleSetClass,
org.semanticweb.owlapi.model.OWLClass enrichedClass) |
Double |
calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass sampleSetClass,
org.semanticweb.owlapi.model.OWLClass enrichedClass,
int populationClassSize) |
void |
connectGraph()
Add default edges based on PPI network
add ( a1 , a2 ) to E
where ( g1 , g2 ) is in PPI, and
a = (g, _) is in A
|
Map<org.semanticweb.owlapi.model.OWLClass,Double> |
fetchScoredCandidateProcesses(org.semanticweb.owlapi.model.OWLClass disease,
Integer populationClassSize) |
Set<org.semanticweb.owlapi.model.OWLClass> |
getActivityTypes(String g)
Get all activity types a gene enables (i.e.
|
Set<String> |
getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
Gets all genes annotated to cls or descendant via involved-in relations
|
Map<String,Object> |
getGraphStatistics() |
String |
getIdLabelPair(Object k) |
Set<org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom> |
getInferredRelationshipsForGene(String g) |
Set<org.semanticweb.owlapi.model.OWLClass> |
getInferredTypes(String g) |
String |
getLabel(Object k) |
Set<org.semanticweb.owlapi.model.OWLClass> |
getMostSpecificActivityTypes(String g) |
Set<org.semanticweb.owlapi.model.OWLClass> |
getMostSpecificProcessTypes(String g) |
int |
getNumberOfGenes() |
Set<org.semanticweb.owlapi.model.OWLClass> |
getProcessTypes(String g) |
void |
initialize(GafDocument gafdoc,
OWLGraphWrapper g) |
void |
normalizeDirections()
Reroute all has_parts to part_ofs
|
static <K,V extends Comparable<? super V>> |
sortByValue(Map<K,V> map) |
addTriple, anonymizeIndividuals, anonymizeIndividualsNotIn, anonymizeIndividualsNotIn, collapseIndividuals, extractModule, generateAllNecessaryIndividuals, generateAllNecessaryIndividuals, generateNecessaryIndividuals, generateNecessaryIndividuals, generateNecessaryIndividuals, getDirectExclusionSet, getExclusionSet, getExistentialRelationships, getExistentialRelationships, getExistentialRelationships, getGeneratedIndividuals, getInclusionSet, getIndividualsInProperPath, getIndividualsInProperPath, getModel, getMostSpecificClassExpression, getMostSpecificClassExpression, getMostSpecificClassExpression, getPrototypeClass, getQueryClassMap, getSuperClassExpressions, hasCycle, hasCycle, isAssertInverses, isPrecomputePropertyClassCombinations, isRemoveAmbiguousIndividuals, mergeInto, normalizeDirections, performTransitiveReduction, performTransitiveReduction, setAssertInverses, setContextualizingSuffix, setDirectExclusionSet, setExclusionSet, setInclusionSet, setPrecomputePropertyClassCombinations, setRemoveAmbiguousIndividuals
public Set<org.semanticweb.owlapi.model.OWLClass> processClassSet
public LegoModelGenerator(ModelContainer model) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
model
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public void initialize(GafDocument gafdoc, OWLGraphWrapper g)
gafdoc
- (optional)g
- public void buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls, Collection<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processCls
- seedGenes
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public void anonymizeMaterialEntities()
public void buildNetwork(String processClsId, Collection<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processClsId
- seedGenes
- org.semanticweb.owlapi.model.OWLOntologyCreationException
public void addGenes(String processClsId, Collection<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void addGenes(org.semanticweb.owlapi.model.OWLClass processCls) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processCls
- org.semanticweb.owlapi.model.OWLOntologyCreationException
seedGraph(String p, Set seed)
public void addGenes(org.semanticweb.owlapi.model.OWLClass processCls, Collection<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processCls
- seedGenes
- org.semanticweb.owlapi.model.OWLOntologyCreationException
org.apache.commons.math.MathException
public void connectGraph()
public void normalizeDirections()
public Map<org.semanticweb.owlapi.model.OWLClass,Double> fetchScoredCandidateProcesses(org.semanticweb.owlapi.model.OWLClass disease, Integer populationClassSize)
public static <K,V extends Comparable<? super V>> Map<K,V> sortByValue(Map<K,V> map)
public Double calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass sampleSetClass, org.semanticweb.owlapi.model.OWLClass enrichedClass) throws org.apache.commons.math.MathException
org.apache.commons.math.MathException
public Double calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass sampleSetClass, org.semanticweb.owlapi.model.OWLClass enrichedClass, int populationClassSize) throws org.apache.commons.math.MathException
org.apache.commons.math.MathException
public Double calculateConditionalProbaility(org.semanticweb.owlapi.model.OWLClass wholeCls, org.semanticweb.owlapi.model.OWLClass partCls)
public Set<org.semanticweb.owlapi.model.OWLClass> getActivityTypes(String g)
g
- public Set<org.semanticweb.owlapi.model.OWLClass> getMostSpecificActivityTypes(String g)
g
- public Set<org.semanticweb.owlapi.model.OWLClass> getMostSpecificProcessTypes(String g)
public Set<org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom> getInferredRelationshipsForGene(String g)
public Set<String> getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
t
- public int getNumberOfGenes()
public String getLabel(Object k)
id
- Copyright © 2010–2015. All rights reserved.