owltools.gaf.lego
Class NetworkInferenceEngine

java.lang.Object
  extended by owltools.gaf.lego.NetworkInferenceEngine

Deprecated.

@Deprecated
public class NetworkInferenceEngine
extends Object

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.

Definitions

Algorithm

TODO


Nested Class Summary
 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.  
 
Field Summary
 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 Summary
NetworkInferenceEngine()
          Deprecated.  
 
Method Summary
 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 = to A where f = argmax(p) { t : t ∈ TA, p=Prob( t | g) }
 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.  
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

activityNetwork

public NetworkInferenceEngine.ActivityNetwork activityNetwork
Deprecated. 
EA ⊆ A x A x TA


processClassSet

public Set<org.semanticweb.owlapi.model.OWLClass> processClassSet
Deprecated. 

partonomy

public NetworkInferenceEngine.Partonomy partonomy
Deprecated. 
M ⊆ N x N, N = A ∪ P


owlOntologyManager

public org.semanticweb.owlapi.model.OWLOntologyManager owlOntologyManager
Deprecated. 

mmg

public MinimalModelGenerator mmg
Deprecated. 
Constructor Detail

NetworkInferenceEngine

public NetworkInferenceEngine()
Deprecated. 
Method Detail

buildNetwork

public void buildNetwork(org.semanticweb.owlapi.model.OWLClass processCls,
                         Set<String> seedGenes)
                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 
Performs all steps to build activation network

Parameters:
processCls -
seedGenes -
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

buildNetwork

public void buildNetwork(String processClsId,
                         Set<String> seedGenes)
                  throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

seedGraph

public void seedGraph(org.semanticweb.owlapi.model.OWLClass processCls,
                      Set<String> seedGenes)
               throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 
Create initial activation node set A for a process P and a set of seed genes for all g ∈ Gseed, add a = to A where f = argmax(p) { t : t ∈ TA, p=Prob( t | g) }

Parameters:
processCls -
seedGenes -
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

seedGraph

public void seedGraph(String processClsId,
                      Set<String> seedGenes)
               throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

seedGraph

public void seedGraph(org.semanticweb.owlapi.model.OWLClass processCls)
               throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 
Parameters:
processCls -
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException
See Also:
seedGraph(String p, Set seed)

createPartonomy

public 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. This partonomy may not be identical to the GO partonomy - each node is an instance in the context of the larger process. As a starting point we have a set of leaves - candidate activations we suspect to be involved somehow in the larger process. We also have knowledge in the ontology - both top-down (e.g. W has_part some P) and bottom-up (e.g. P part_of some W). We want to connect the leaves to the roots through intermediates. TODO: MAPKK activity part_of activation of MAPK +reg MAPK activity

Parameters:
processCls -

inferLocations

public void inferLocations()
Deprecated. 

connectGraph

public 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


getMostLikelyActivityForGene

public NetworkInferenceEngine.Activity getMostLikelyActivityForGene(String g,
                                                                    org.semanticweb.owlapi.model.OWLClass processCls)
Deprecated. 
Parameters:
g -
processCls -
Returns:

calculateConditionalProbaility

public Double calculateConditionalProbaility(org.semanticweb.owlapi.model.OWLClass wholeCls,
                                             org.semanticweb.owlapi.model.OWLClass partCls)
Deprecated. 
Pr( F | P ) = Pr(F,P) / Pr(P)


getActivityTypes

public Set<org.semanticweb.owlapi.model.OWLClass> getActivityTypes(String g)
Deprecated. 
Get all activity types a gene enables (i.e. direct MF annotations)

Parameters:
g -
Returns:
{ t : t ∈ TA, g x t ∈ Enables }

getMostSpecificActivityTypes

public Set<org.semanticweb.owlapi.model.OWLClass> getMostSpecificActivityTypes(String g)
Deprecated. 
Parameters:
g -
Returns:
{ t : t ∈ getActivityTypes(g), ¬ ∃ t' : t' ∈ getActivityTypes(g), t' ProperInferredßSubClassOf t }

getProcessTypes

public Set<org.semanticweb.owlapi.model.OWLClass> getProcessTypes(String g)
Deprecated. 

getGenes

public Set<String> getGenes(org.semanticweb.owlapi.model.OWLClass wholeCls)
Deprecated. 
Gets all genes that enable a given activity type (i.e. inverred annotations to MF term)

Parameters:
t -
Returns:
{ g : g x t ∈ InferredInvolvedIn }

getNumberOfGenes

public int getNumberOfGenes()
Deprecated. 
Returns:
|G|

initialize

public void initialize(GafDocument gafdoc,
                       OWLGraphWrapper g)
Deprecated. 

getLabel

public String getLabel(Object k)
Deprecated. 
Parameters:
id -
Returns:
label for any class or entity in the graph

getGraphStatistics

public Map<String,Object> getGraphStatistics()
Deprecated. 

translateNetworkToOWL

@Deprecated
public org.semanticweb.owlapi.model.OWLOntology translateNetworkToOWL()
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 

Translates ontological activation network into OWL (aka lego model) Notes: we treat all members of G as proteins, but these may be other kinds of gene product. Note also the source ID may be a gene ID. In this case we can substitute "enabled_by some g" with "enabled_by some (product_of some g)" In some cases the edge type is not known - here we can use a generic owlTopProperty - or we can assume an activates relation, and leave the user to prune/modify Warning: may possibly be refactored into a separate writer class.

Returns:
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException

translateNetworkToOWL

public org.semanticweb.owlapi.model.OWLOntology translateNetworkToOWL(org.semanticweb.owlapi.model.OWLOntology ont)
                                                               throws org.semanticweb.owlapi.model.OWLOntologyCreationException
Deprecated. 
Throws:
org.semanticweb.owlapi.model.OWLOntologyCreationException


Copyright © 2010-2014. All Rights Reserved.