Package 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 Details

    • PatternBox

      public PatternBox()

  • Method Details

    • 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