org.biopax.paxtools.pattern

Class PatternBox

java.lang.Object

org.biopax.paxtools.pattern.PatternBox

public class PatternBox
extends Object

This class contains several pattern samples.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
PatternBox()

Method Summary

Modifier and Type	Method and Description
static Pattern	actChange(boolean activating, Map<EntityReference,Set<ModificationFeature>> activityFeat, Map<EntityReference,Set<ModificationFeature>> inactivityFeat) Pattern for the activity of an EntityReference is changed through a Conversion.
static Pattern	bindsTo() Finds two Protein that appear together in a Complex.
static Pattern	catalysisPrecedes(Blacklist blacklist) Pattern for detecting two EntityReferences are controlling consecutive reactions, where output of one reaction is input to the other.
static Pattern	chemicalAffectsProteinThroughBinding(Blacklist blacklist) A small molecule is in a complex with a protein.
static Pattern	chemicalAffectsProteinThroughControl() A small molecule controls an interaction of which the protein is a participant.
static Pattern	controlsDegradationIndirectly() Finds cases where protein A changes state of B, and B is then degraded.
static Pattern	controlsExpressionWithConversion() Finds the cases where transcription relation is shown using a Conversion instead of a TemplateReaction.
static Pattern	controlsExpressionWithTemplateReac() Finds transcription factors that trans-activate or trans-inhibit an entity.
static Pattern	controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption) Pattern for a Protein controlling a reaction whose participant is a small molecule.
static Pattern	controlsPhosphorylation()
static Pattern	controlsStateChange() Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
static Pattern	controlsStateChangeBothControlAndPart() Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
static Pattern	controlsStateChangeButIsParticipant() Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.
static Pattern	controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist) Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
static Pattern	controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist) Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.
static Pattern	controlsStateChangeThroughDegradation() Finds cases where proteins affect their degradation.
static Pattern	controlsTransport() Pattern for a ProteinReference has a member PhysicalEntity that is controlling a transportation of another ProteinReference.
static Pattern	controlsTransportOfChemical(Blacklist blacklist) Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction that changes cellular location of a small molecule.
static Pattern	hasNonSelfEffect() Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not associated with the EntityReference of the initial PhysicalEntity.
static Pattern	inComplexWith() Two proteins have states that are members of the same complex.
static Pattern	inSameActiveComplex() Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has an activity.
static Pattern	inSameComplex() Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
static Pattern	inSameComplexEffectingConversion() Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex is controlling a Conversion.
static Pattern	inSameComplexHavingTransActivity() Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has transcriptional activity.
static Pattern	modifiedPESimple() Pattern for an EntityReference has distinct PhysicalEntities associated with both left and right of a Conversion.
static Pattern	modifierConv() Pattern for finding Conversions that an EntityReference is participating.
static Pattern	molecularInteraction() Constructs a pattern where first and last molecules are participants of a MolecularInteraction.
static Pattern	neighborOf() Constructs a pattern where first and last proteins are related through an interaction.
static Pattern	peInOut()
static Pattern	reactsWith(Blacklist blacklist) Constructs a pattern where first and last small molecules are substrates to the same biochemical reaction.
static Pattern	relatedProteinRefOfInter(Class<? extends Interaction>... seedType) Finds ProteinsReference related to an interaction.
static Pattern	stateChange(Pattern p, String ctrlLabel) Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that belongs to the same EntityReference.
static Pattern	usedToProduce(Blacklist blacklist) Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PatternBox

public PatternBox()

Method Detail

controlsStateChange

public static Pattern controlsStateChange()

Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference.

Returns:

the pattern

controlsTransport

public static Pattern controlsTransport()

Pattern for a ProteinReference has a member PhysicalEntity that is controlling a transportation of another ProteinReference.

Returns:

the pattern

controlsTransportOfChemical

public static Pattern controlsTransportOfChemical(Blacklist blacklist)

Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction that changes cellular location of a small molecule.

Parameters:

blacklist - a skip-list of ubiquitous molecules

Returns:

the pattern

controlsStateChangeBothControlAndPart

public static Pattern controlsStateChangeBothControlAndPart()

Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference. In this case the controller is also an input to the reaction. The affected protein is the one that is represented with different non-generic physical entities at left and right of the reaction.

Returns:

the pattern

controlsStateChangeButIsParticipant

public static Pattern controlsStateChangeButIsParticipant()

Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change reaction of another EntityReference. This pattern is different from the original controls-state-change. The controller in this case is not modeled as a controller, but as a participant of the conversion, and it is at both sides.

Returns:

the pattern

stateChange

public static Pattern stateChange(Pattern p,
                                  String ctrlLabel)

Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that belongs to the same EntityReference.

Parameters:

p - pattern to update

ctrlLabel - label

Returns:

the pattern

controlsStateChangeThroughControllerSmallMolecule

public static Pattern controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist)

Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.

Parameters:

blacklist - a skip-list of ubiquitous molecules

Returns:

the pattern

controlsStateChangeThroughBindingSmallMolecule

public static Pattern controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist)

Pattern for an entity is producing a small molecule, and the small molecule controls state change of another molecule.

Parameters:

blacklist - a skip-list of ubiquitous molecules

Returns:

the pattern

controlsStateChangeThroughDegradation

public static Pattern controlsStateChangeThroughDegradation()

Finds cases where proteins affect their degradation.

Returns:

the pattern

controlsPhosphorylation

public static Pattern controlsPhosphorylation()

controlsMetabolicCatalysis

public static Pattern controlsMetabolicCatalysis(Blacklist blacklist,
                                                 boolean consumption)

Pattern for a Protein controlling a reaction whose participant is a small molecule.

Parameters:

blacklist - a skip-list of ubiquitous molecules

consumption - true/false (TODO explain)

Returns:

the pattern

catalysisPrecedes

public static Pattern catalysisPrecedes(Blacklist blacklist)

Pattern for detecting two EntityReferences are controlling consecutive reactions, where output of one reaction is input to the other.

Parameters:

blacklist - to detect ubiquitous small molecules

Returns:

the pattern

controlsExpressionWithTemplateReac

public static Pattern controlsExpressionWithTemplateReac()

Finds transcription factors that trans-activate or trans-inhibit an entity.

Returns:

the pattern

controlsExpressionWithConversion

public static Pattern controlsExpressionWithConversion()

Finds the cases where transcription relation is shown using a Conversion instead of a TemplateReaction.

Returns:

the pattern

controlsDegradationIndirectly

public static Pattern controlsDegradationIndirectly()

Finds cases where protein A changes state of B, and B is then degraded. NOTE: THIS PATTERN DOES NOT WORK. KEEPING ONLY FOR HISTORICAL REASONS.

Returns:

the pattern

inComplexWith

public static Pattern inComplexWith()

Two proteins have states that are members of the same complex. Handles nested complexes and homologies. Also guarantees that relationship to the complex is through different direct complex members.

Returns:

pattern

chemicalAffectsProteinThroughBinding

public static Pattern chemicalAffectsProteinThroughBinding(Blacklist blacklist)

A small molecule is in a complex with a protein.

Parameters:

blacklist - a skip-list of ubiquitous molecules

Returns:

pattern

chemicalAffectsProteinThroughControl

public static Pattern chemicalAffectsProteinThroughControl()

A small molecule controls an interaction of which the protein is a participant.

Returns:

pattern

neighborOf

public static Pattern neighborOf()

Constructs a pattern where first and last proteins are related through an interaction. They can be participants or controllers. No limitation.

Returns:

the pattern

reactsWith

public static Pattern reactsWith(Blacklist blacklist)

Constructs a pattern where first and last small molecules are substrates to the same biochemical reaction.

Parameters:

blacklist - a skip-list of ubiquitous molecules

Returns:

the pattern

usedToProduce

public static Pattern usedToProduce(Blacklist blacklist)

Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule. biochemical reaction.

Parameters:

blacklist - a skip-list of ubiquitous molecules

Returns:

the pattern

molecularInteraction

public static Pattern molecularInteraction()

Constructs a pattern where first and last molecules are participants of a MolecularInteraction.

Returns:

the pattern

relatedProteinRefOfInter

public static Pattern relatedProteinRefOfInter(Class<? extends Interaction>... seedType)

Finds ProteinsReference related to an interaction. If specific types of interactions are desired, they should be sent as parameter, otherwise leave the parameter empty.

Parameters:

seedType - specific BioPAX interaction sub-types (interface classes)

Returns:

pattern

inSameComplex

public static Pattern inSameComplex()

Pattern for two different EntityReference have member PhysicalEntity in the same Complex. Complex membership can be through multiple nesting and/or through homology relations.

Returns:

the pattern

inSameActiveComplex

public static Pattern inSameActiveComplex()

Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has an activity. Complex membership can be through multiple nesting and/or through homology relations.

Returns:

the pattern

inSameComplexHavingTransActivity

public static Pattern inSameComplexHavingTransActivity()

Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex has transcriptional activity. Complex membership can be through multiple nesting and/or through homology relations.

Returns:

the pattern

inSameComplexEffectingConversion

public static Pattern inSameComplexEffectingConversion()

Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and the Complex is controlling a Conversion. Complex membership can be through multiple nesting and/or through homology relations.

Returns:

the pattern

peInOut

public static Pattern peInOut()

modifiedPESimple

public static Pattern modifiedPESimple()

Pattern for an EntityReference has distinct PhysicalEntities associated with both left and right of a Conversion.

Returns:

the pattern

actChange

public static Pattern actChange(boolean activating,
                                Map<EntityReference,Set<ModificationFeature>> activityFeat,
                                Map<EntityReference,Set<ModificationFeature>> inactivityFeat)

Pattern for the activity of an EntityReference is changed through a Conversion.

Parameters:

activating - desired change

activityFeat - modification features associated with activity

inactivityFeat - modification features associated with inactivity

Returns:

the pattern

modifierConv

public static Pattern modifierConv()

Pattern for finding Conversions that an EntityReference is participating.

Returns:

the pattern

hasNonSelfEffect

public static Pattern hasNonSelfEffect()

Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not associated with the EntityReference of the initial PhysicalEntity.

Returns:

the pattern

bindsTo

public static Pattern bindsTo()

Finds two Protein that appear together in a Complex.

Returns:

the pattern