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java.lang.Objectowltools.util.MinimalModelGenerator
owltools.gaf.lego.LegoModelGenerator
public class LegoModelGenerator
Generates a Functional Network (aka LEGO) graphĂ for a process given an ontology and a set of annotations. A process can be a 'normal' biological process (e.g. from GO) or a pathological process (we can treat MP as abnormal processes for the purposes of this analysis, or make a parallel ontology) The input is a process class and a set of genes (e.g. all genes involved in that BP), construct the most likely set of gene + activity-type (i.e. MF) pairs that are likely to be executed during this process. Also infer causal relationships between gene-activity pairs based on PPI networks, annotation extensions. The network generation is broken into two steps
#seedGraph
- seed initial A
#createPartonomy
- create partonomy P
connectGraph()
- created activity network E
Field Summary | |
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Set<org.semanticweb.owlapi.model.OWLClass> |
processClassSet
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Fields inherited from class owltools.util.MinimalModelGenerator |
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prototypeIndividualMap |
Constructor Summary | |
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LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox)
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LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox,
org.semanticweb.owlapi.model.OWLOntology abox)
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LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox,
org.semanticweb.owlapi.model.OWLOntology abox,
org.semanticweb.owlapi.reasoner.OWLReasonerFactory rf)
Deprecated. |
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LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox,
org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory)
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Method Summary | ||
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void |
addGenes(org.semanticweb.owlapi.model.OWLClass processCls)
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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 = |
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void |
addGenes(String processClsId,
Collection<String> seedGenes)
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void |
buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls,
Collection<String> seedGenes)
Performs all steps to build activation network |
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void |
buildNetwork(String processClsId,
Collection<String> seedGenes)
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Double |
calculateConditionalProbaility(org.semanticweb.owlapi.model.OWLClass wholeCls,
org.semanticweb.owlapi.model.OWLClass partCls)
Pr( F | P ) = Pr(F,P) / Pr(P) |
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Double |
calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass sampleSetClass,
org.semanticweb.owlapi.model.OWLClass enrichedClass)
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Double |
calculatePairwiseEnrichment(org.semanticweb.owlapi.model.OWLClass sampleSetClass,
org.semanticweb.owlapi.model.OWLClass enrichedClass,
int populationClassSize)
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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 |
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Map<org.semanticweb.owlapi.model.OWLClass,Double> |
fetchScoredCandidateProcesses(org.semanticweb.owlapi.model.OWLClass disease,
Integer populationClassSize)
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Set<org.semanticweb.owlapi.model.OWLClass> |
getActivityTypes(String g)
Get all activity types a gene enables (i.e. |
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Set<String> |
getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
Gets all genes annotated to cls or descendant via involved-in relations |
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Map<String,Object> |
getGraphStatistics()
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String |
getIdLabelPair(Object k)
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Set<org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom> |
getInferredRelationshipsForGene(String g)
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Set<org.semanticweb.owlapi.model.OWLClass> |
getInferredTypes(String g)
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String |
getLabel(Object k)
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Set<org.semanticweb.owlapi.model.OWLClass> |
getMostSpecificActivityTypes(String g)
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Set<org.semanticweb.owlapi.model.OWLClass> |
getMostSpecificProcessTypes(String g)
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int |
getNumberOfGenes()
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Set<org.semanticweb.owlapi.model.OWLClass> |
getProcessTypes(String g)
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void |
initialize(GafDocument gafdoc,
OWLGraphWrapper g)
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void |
normalizeDirections()
Reroute all has_parts to part_ofs |
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static
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sortByValue(Map<K,V> map)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public Set<org.semanticweb.owlapi.model.OWLClass> processClassSet
Constructor Detail |
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public LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
tbox
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org.semanticweb.owlapi.model.OWLOntologyCreationException
@Deprecated public LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox, org.semanticweb.owlapi.model.OWLOntology abox, org.semanticweb.owlapi.reasoner.OWLReasonerFactory rf) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
tbox
- abox
- rf
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org.semanticweb.owlapi.model.OWLOntologyCreationException
public LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox, org.semanticweb.owlapi.model.OWLOntology abox) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
tbox
- abox
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org.semanticweb.owlapi.model.OWLOntologyCreationException
public LegoModelGenerator(org.semanticweb.owlapi.model.OWLOntology tbox, org.semanticweb.owlapi.reasoner.OWLReasonerFactory reasonerFactory) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
tbox
- reasonerFactory
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org.semanticweb.owlapi.model.OWLOntologyCreationException
Method Detail |
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public void initialize(GafDocument gafdoc, OWLGraphWrapper g)
gafdoc
- g
- public void buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls, Collection<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processCls
- seedGenes
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org.semanticweb.owlapi.model.OWLOntologyCreationException
public void buildNetwork(String processClsId, Collection<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
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
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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
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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
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public Set<org.semanticweb.owlapi.model.OWLClass> getMostSpecificActivityTypes(String g)
g
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public Set<org.semanticweb.owlapi.model.OWLClass> getMostSpecificProcessTypes(String g)
public Set<org.semanticweb.owlapi.model.OWLClass> getProcessTypes(String g)
public Set<org.semanticweb.owlapi.model.OWLClass> getInferredTypes(String g)
public Set<org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom> getInferredRelationshipsForGene(String g)
public Set<String> getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
t
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public int getNumberOfGenes()
public String getLabel(Object k)
id
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public String getIdLabelPair(Object k)
public Map<String,Object> getGraphStatistics()
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