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java.lang.Objectowltools.gaf.lego.NetworkInferenceEngine
public class NetworkInferenceEngine
Generates a Ontological Functional Network (aka LEGO graph) for a process given an ontology and a set of annotations The input is a GO BP 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. Finally, break the process into chunks, e.g. using has_part links.
seedGraph(org.semanticweb.owlapi.model.OWLClass, java.util.Set)
- seed initial A
createPartonomy(org.semanticweb.owlapi.model.OWLClass)
- create partonomy P
connectGraph()
- created activity network E
Nested Class Summary | |
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class |
NetworkInferenceEngine.Activity
A ⊆ G x TA An instance of an activity that is enabled by some gene/product |
class |
NetworkInferenceEngine.ActivityNetwork
NA = (A, EA) A network/graph of activity nodes |
class |
NetworkInferenceEngine.Edge<T extends NetworkInferenceEngine.InstanceNode,U extends NetworkInferenceEngine.InstanceNode>
EdgeType can be null for unknown (i.e. |
class |
NetworkInferenceEngine.InstanceNode
|
class |
NetworkInferenceEngine.Partonomy
M : Merelogy (partonomy), from activity instances to process instances, and between process instances. |
class |
NetworkInferenceEngine.Process
|
Field Summary | |
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NetworkInferenceEngine.ActivityNetwork |
activityNetwork
EA ⊆ A x A x TA |
MinimalModelGenerator |
mmg
|
org.semanticweb.owlapi.model.OWLOntologyManager |
owlOntologyManager
|
NetworkInferenceEngine.Partonomy |
partonomy
M ⊆ N x N, N = A ∪ P |
Set<org.semanticweb.owlapi.model.OWLClass> |
processClassSet
|
Constructor Summary | |
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NetworkInferenceEngine()
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Method Summary | |
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void |
buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls,
Set<String> seedGenes)
Performs all steps to build activation network |
void |
buildNetwork(String processClsId,
Set<String> seedGenes)
|
Double |
calculateConditionalProbaility(org.semanticweb.owlapi.model.OWLClass wholeCls,
org.semanticweb.owlapi.model.OWLClass partCls)
Pr( F | P ) = Pr(F,P) / Pr(P) |
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 |
void |
createPartonomy(org.semanticweb.owlapi.model.OWLClass processCls)
Generate M = N x N where N ∈ P or N ∈ A Basic idea: we want to create a partonomy that breaks down a large process into smaller chunks and ultimately partonomic leaves - activities. |
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 that enable a given activity type (i.e. |
Map<String,Object> |
getGraphStatistics()
|
String |
getLabel(Object k)
|
NetworkInferenceEngine.Activity |
getMostLikelyActivityForGene(String g,
org.semanticweb.owlapi.model.OWLClass processCls)
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getMostSpecificActivityTypes(String g)
|
int |
getNumberOfGenes()
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getProcessTypes(String g)
|
void |
inferLocations()
|
void |
initialize(GafDocument gafdoc,
OWLGraphWrapper g)
|
void |
seedGraph(org.semanticweb.owlapi.model.OWLClass processCls)
|
void |
seedGraph(org.semanticweb.owlapi.model.OWLClass processCls,
Set<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 |
seedGraph(String processClsId,
Set<String> seedGenes)
|
org.semanticweb.owlapi.model.OWLOntology |
translateNetworkToOWL()
Deprecated. |
org.semanticweb.owlapi.model.OWLOntology |
translateNetworkToOWL(org.semanticweb.owlapi.model.OWLOntology ont)
|
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 NetworkInferenceEngine.ActivityNetwork activityNetwork
public Set<org.semanticweb.owlapi.model.OWLClass> processClassSet
public NetworkInferenceEngine.Partonomy partonomy
public org.semanticweb.owlapi.model.OWLOntologyManager owlOntologyManager
public MinimalModelGenerator mmg
Constructor Detail |
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public NetworkInferenceEngine()
Method Detail |
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public void buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls, Set<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processCls
- seedGenes
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void buildNetwork(String processClsId, Set<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void seedGraph(org.semanticweb.owlapi.model.OWLClass processCls, Set<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
processCls
- seedGenes
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void seedGraph(String processClsId, Set<String> seedGenes) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void seedGraph(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 createPartonomy(org.semanticweb.owlapi.model.OWLClass processCls)
processCls
- public void inferLocations()
public void connectGraph()
public NetworkInferenceEngine.Activity getMostLikelyActivityForGene(String g, org.semanticweb.owlapi.model.OWLClass processCls)
g
- processCls
-
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> getProcessTypes(String g)
public Set<String> getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
t
-
public int getNumberOfGenes()
public void initialize(GafDocument gafdoc, OWLGraphWrapper g)
public String getLabel(Object k)
id
-
public Map<String,Object> getGraphStatistics()
@Deprecated public org.semanticweb.owlapi.model.OWLOntology translateNetworkToOWL() throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public org.semanticweb.owlapi.model.OWLOntology translateNetworkToOWL(org.semanticweb.owlapi.model.OWLOntology ont) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
|
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