@Deprecated public class NetworkInferenceEngine extends Object
seedGraph(org.semanticweb.owlapi.model.OWLClass, java.util.Set<java.lang.String>)
- seed initial A
createPartonomy(org.semanticweb.owlapi.model.OWLClass)
- create partonomy P
connectGraph()
- created activity network E
Modifier and Type | Class and Description |
---|---|
class |
NetworkInferenceEngine.Activity
Deprecated.
A ⊆ G x TA
An instance of an activity that is enabled by some gene/product
|
class |
NetworkInferenceEngine.ActivityNetwork
Deprecated.
NA = (A, EA)
A network/graph of activity nodes
|
class |
NetworkInferenceEngine.Edge<T extends NetworkInferenceEngine.InstanceNode,U extends NetworkInferenceEngine.InstanceNode>
Deprecated.
EdgeType can be null for unknown (i.e.
|
class |
NetworkInferenceEngine.InstanceNode
Deprecated.
|
class |
NetworkInferenceEngine.Partonomy
Deprecated.
M : Merelogy (partonomy), from activity instances to process instances, and between process instances.
|
class |
NetworkInferenceEngine.Process
Deprecated.
|
Modifier and Type | Field and Description |
---|---|
NetworkInferenceEngine.ActivityNetwork |
activityNetwork
Deprecated.
EA ⊆ A x A x TA
|
MinimalModelGenerator |
mmg
Deprecated.
|
org.semanticweb.owlapi.model.OWLOntologyManager |
owlOntologyManager
Deprecated.
|
NetworkInferenceEngine.Partonomy |
partonomy
Deprecated.
M ⊆ N x N, N = A ∪ P
|
Set<org.semanticweb.owlapi.model.OWLClass> |
processClassSet
Deprecated.
|
Constructor and Description |
---|
NetworkInferenceEngine()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
void |
buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls,
Set<String> seedGenes)
Deprecated.
Performs all steps to build activation network
|
void |
buildNetwork(String processClsId,
Set<String> seedGenes)
Deprecated.
|
Double |
calculateConditionalProbaility(org.semanticweb.owlapi.model.OWLClass wholeCls,
org.semanticweb.owlapi.model.OWLClass partCls)
Deprecated.
Pr( F | P ) = Pr(F,P) / Pr(P)
|
void |
connectGraph()
Deprecated.
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)
Deprecated.
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)
Deprecated.
Get all activity types a gene enables (i.e.
|
Set<String> |
getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
Deprecated.
Gets all genes that enable a given activity type (i.e.
|
Map<String,Object> |
getGraphStatistics()
Deprecated.
|
String |
getLabel(Object k)
Deprecated.
|
NetworkInferenceEngine.Activity |
getMostLikelyActivityForGene(String g,
org.semanticweb.owlapi.model.OWLClass processCls)
Deprecated.
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getMostSpecificActivityTypes(String g)
Deprecated.
|
int |
getNumberOfGenes()
Deprecated.
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getProcessTypes(String g)
Deprecated.
|
void |
inferLocations()
Deprecated.
|
void |
initialize(GafDocument gafdoc,
OWLGraphWrapper g)
Deprecated.
|
void |
seedGraph(org.semanticweb.owlapi.model.OWLClass processCls)
Deprecated.
|
void |
seedGraph(org.semanticweb.owlapi.model.OWLClass processCls,
Set<String> seedGenes)
Deprecated.
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)
Deprecated.
|
org.semanticweb.owlapi.model.OWLOntology |
translateNetworkToOWL()
Deprecated.
|
org.semanticweb.owlapi.model.OWLOntology |
translateNetworkToOWL(org.semanticweb.owlapi.model.OWLOntology ont)
Deprecated.
|
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
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
- @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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