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fr.curie.BiNoM.pathways.biopax
Interface control

All Superinterfaces:
entity, interaction, physicalInteraction, com.ibm.adtech.jastor.Thing
All Known Subinterfaces:
catalysis, modulation
All Known Implementing Classes:
catalysisImpl, controlImpl, modulationImpl
public interface control
extends physicalInteraction, com.ibm.adtech.jastor.Thing

Interface for control ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

(URI: http://www.biopax.org/release/biopax-level2.owl#control)


RDF Schema Standard Properties
comment : Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition. Comment: In general, the targets of control processes (i.e. occupants of the CONTROLLED property) should be interactions. Conceptually, physical entities are involved in interactions (or events) and the events should be controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction that can be ambiguous out of context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a reaction in which the substrate is phosphorylated, instead of as a control interaction in which the kinase activates the substrate. Since this class is a superclass for specific types of control, instances of the control class should only be created when none of its subclasses are applicable. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism controls the pathway.^^http://www.w3.org/2001/XMLSchema#string


Field Summary
static com.hp.hpl.jena.rdf.model.Property CONTROL_DASH_TYPEProperty
          The Jena Property for CONTROL_DASH_TYPE
static com.hp.hpl.jena.rdf.model.Property CONTROLLEDProperty
          The Jena Property for CONTROLLED
static com.hp.hpl.jena.rdf.model.Property CONTROLLERProperty
          The Jena Property for CONTROLLER
static com.hp.hpl.jena.rdf.model.Resource TYPE
          The rdf:type for this ontology class
 
Fields inherited from interface fr.curie.BiNoM.pathways.biopax.physicalInteraction
INTERACTION_DASH_TYPEProperty
 
Fields inherited from interface fr.curie.BiNoM.pathways.biopax.interaction
EVIDENCEProperty, PARTICIPANTSProperty
 
Fields inherited from interface fr.curie.BiNoM.pathways.biopax.entity
AVAILABILITYProperty, COMMENTProperty, DATA_DASH_SOURCEProperty, NAMEProperty, SHORT_DASH_NAMEProperty, SYNONYMSProperty, XREFProperty
 
Fields inherited from interface com.ibm.adtech.jastor.Thing
copyright
 
Method Summary
 java.lang.String getCONTROL_DASH_TYPE()
          Gets the 'CONTROL_DASH_TYPE' property value
 interaction getCONTROLLED_asinteraction()
          Gets the 'CONTROLLED' property value
 pathway getCONTROLLED_aspathway()
          Gets the 'CONTROLLED' property value
 physicalEntityParticipant getCONTROLLER()
          Gets the 'CONTROLLER' property value
 void setCONTROL_DASH_TYPE(java.lang.String CONTROL_DASH_TYPE)
          Sets the 'CONTROL_DASH_TYPE' property value
 interaction setCONTROLLED_asinteraction()
          Sets the 'CONTROLLED' property value to an anonymous node
 interaction setCONTROLLED_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)
          Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.
 pathway setCONTROLLED_aspathway()
          Sets the 'CONTROLLED' property value to an anonymous node
 pathway setCONTROLLED_aspathway(com.hp.hpl.jena.rdf.model.Resource resource)
          Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.
 void setCONTROLLED(interaction CONTROLLED)
          Sets the 'CONTROLLED' property value
 void setCONTROLLED(pathway CONTROLLED)
          Sets the 'CONTROLLED' property value
 physicalEntityParticipant setCONTROLLER()
          Sets the 'CONTROLLER' property value to an anonymous node
 void setCONTROLLER(physicalEntityParticipant CONTROLLER)
          Sets the 'CONTROLLER' property value
 physicalEntityParticipant setCONTROLLER(com.hp.hpl.jena.rdf.model.Resource resource)
          Sets the 'CONTROLLER' property value to the given resource, and add's rdf:type properties.
 
Methods inherited from interface fr.curie.BiNoM.pathways.biopax.physicalInteraction
addINTERACTION_DASH_TYPE, addINTERACTION_DASH_TYPE, addINTERACTION_DASH_TYPE, addPARTICIPANTS_asphysicalEntityParticipant, addPARTICIPANTS_asphysicalEntityParticipant, addPARTICIPANTS, getINTERACTION_DASH_TYPE, getPARTICIPANTS_asphysicalEntityParticipant, removeINTERACTION_DASH_TYPE, removePARTICIPANTS
 
Methods inherited from interface fr.curie.BiNoM.pathways.biopax.interaction
addEVIDENCE, addEVIDENCE, addEVIDENCE, addPARTICIPANTS_asentity, addPARTICIPANTS_asentity, addPARTICIPANTS, getEVIDENCE, getPARTICIPANTS_asentity, removeEVIDENCE, removePARTICIPANTS
 
Methods inherited from interface fr.curie.BiNoM.pathways.biopax.entity
addAVAILABILITY, addCOMMENT, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addSYNONYMS, addXREF, addXREF, addXREF, getAVAILABILITY, getCOMMENT, getDATA_DASH_SOURCE, getNAME, getSHORT_DASH_NAME, getSYNONYMS, getXREF, removeAVAILABILITY, removeCOMMENT, removeDATA_DASH_SOURCE, removeSYNONYMS, removeXREF, setNAME, setSHORT_DASH_NAME
 
Methods inherited from interface com.ibm.adtech.jastor.Thing
clearCache, isRDFType, listStatements, model, registerListener, removeStatements, resource, unregisterListener, uri
 

Field Detail

TYPE

static final com.hp.hpl.jena.rdf.model.Resource TYPE
The rdf:type for this ontology class

CONTROLLERProperty

static final com.hp.hpl.jena.rdf.model.Property CONTROLLERProperty
The Jena Property for CONTROLLER

(URI: http://www.biopax.org/release/biopax-level2.owl#CONTROLLER)



RDF Schema Standard Properties
comment : The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. CONTROLLER is a sub-property of PARTICIPANTS.@en

CONTROLLEDProperty

static final com.hp.hpl.jena.rdf.model.Property CONTROLLEDProperty
The Jena Property for CONTROLLED

(URI: http://www.biopax.org/release/biopax-level2.owl#CONTROLLED)



RDF Schema Standard Properties
comment : The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme. CONTROLLED is a sub-property of PARTICIPANTS.@en

CONTROL_DASH_TYPEProperty

static final com.hp.hpl.jena.rdf.model.Property CONTROL_DASH_TYPEProperty
The Jena Property for CONTROL_DASH_TYPE

(URI: http://www.biopax.org/release/biopax-level2.owl#CONTROL-TYPE)



RDF Schema Standard Properties
comment : Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities. The following terms are possible values: ACTIVATION: General activation. Compounds that activate the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. The following term can not be used in the catalysis class: INHIBITION: General inhibition. Compounds that inhibit the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper(s) curated thus far do not define the mechanism, and a full literature search has yet to be performed. The following terms can only be used in the modulation class (these definitions from EcoCyc): INHIBITION-ALLOSTERIC Allosteric inhibitors decrease the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that decreases the affinity of the enzyme to its substrates without affecting its VMAX. Allosteric inhibitors can be competitive or noncompetitive inhibitors, therefore, those inhibition categories can be used in conjunction with this category. INHIBITION-COMPETITIVE Competitive inhibitors are compounds that competitively inhibit the specified enzyme activity by binding reversibly to the enzyme and preventing the substrate from binding. Binding of the inhibitor and substrate are mutually exclusive because it is assumed that the inhibitor and substrate can both bind only to the free enzyme. A competitive inhibitor can either bind to the active site of the enzyme, directly excluding the substrate from binding there, or it can bind to another site on the enzyme, altering the conformation of the enzyme such that the substrate can not bind to the active site. INHIBITION-IRREVERSIBLE Irreversible inhibitors are compounds that irreversibly inhibit the specified enzyme activity by binding to the enzyme and dissociating so slowly that it is considered irreversible. For example, alkylating agents, such as iodoacetamide, irreversibly inhibit the catalytic activity of some enzymes by modifying cysteine side chains. INHIBITION-NONCOMPETITIVE Noncompetitive inhibitors are compounds that noncompetitively inhibit the specified enzyme by binding reversibly to both the free enzyme and to the enzyme-substrate complex. The inhibitor and substrate may be bound to the enzyme simultaneously and do not exclude each other. However, only the enzyme-substrate complex (not the enzyme-substrate-inhibitor complex) is catalytically active. INHIBITION-OTHER Compounds that inhibit the specified enzyme activity by a mechanism that has been characterized, but that cannot be clearly classified as irreversible, competitive, noncompetitive, uncompetitive, or allosteric. INHIBITION-UNCOMPETITIVE Uncompetitive inhibitors are compounds that uncompetitively inhibit the specified enzyme activity by binding reversibly to the enzyme-substrate complex but not to the enzyme alone. ACTIVATION-NONALLOSTERIC Nonallosteric activators increase the specified enzyme activity by means other than allosteric. ACTIVATION-ALLOSTERIC Allosteric activators increase the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that increases the affinity of the enzyme to its substrates without affecting its VMAX.^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getCONTROLLER

physicalEntityParticipant getCONTROLLER()
                                        throws com.ibm.adtech.jastor.JastorException
Gets the 'CONTROLLER' property value

Returns:
physicalEntityParticipant
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLERProperty

setCONTROLLER

void setCONTROLLER(physicalEntityParticipant CONTROLLER)
                   throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLER' property value

Parameters:
{@link - fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant}
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLERProperty

setCONTROLLER

physicalEntityParticipant setCONTROLLER()
                                        throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLER' property value to an anonymous node

Returns:
physicalEntityParticipant, the created value
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLERProperty

setCONTROLLER

physicalEntityParticipant setCONTROLLER(com.hp.hpl.jena.rdf.model.Resource resource)
                                        throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLER' property value to the given resource, and add's rdf:type properties. This method is equivalent constructing a new instance of physicalEntityParticipant with the factory. and calling setCONTROLLER(fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant CONTROLLER) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#physicalEntityParticipant. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:
{@link - com.hp.hpl.jena.rdf.model.Resource} must not be be null.
Returns:
physicalEntityParticipant, the newly created value
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLERProperty

getCONTROLLED_asinteraction

interaction getCONTROLLED_asinteraction()
                                        throws com.ibm.adtech.jastor.JastorException
Gets the 'CONTROLLED' property value

Returns:
interaction
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

setCONTROLLED

void setCONTROLLED(interaction CONTROLLED)
                   throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLED' property value

Parameters:
{@link - fr.curie.BiNoM.pathways.biopax.interaction}
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

setCONTROLLED_asinteraction

interaction setCONTROLLED_asinteraction()
                                        throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLED' property value to an anonymous node

Returns:
interaction, the created value
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

setCONTROLLED_asinteraction

interaction setCONTROLLED_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)
                                        throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties. This method is equivalent constructing a new instance of interaction with the factory. and calling setCONTROLLED(fr.curie.BiNoM.pathways.biopax.interaction CONTROLLED) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#interaction. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:
{@link - com.hp.hpl.jena.rdf.model.Resource} must not be be null.
Returns:
interaction, the newly created value
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

getCONTROLLED_aspathway

pathway getCONTROLLED_aspathway()
                                throws com.ibm.adtech.jastor.JastorException
Gets the 'CONTROLLED' property value

Returns:
pathway
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

setCONTROLLED

void setCONTROLLED(pathway CONTROLLED)
                   throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLED' property value

Parameters:
{@link - fr.curie.BiNoM.pathways.biopax.pathway}
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

setCONTROLLED_aspathway

pathway setCONTROLLED_aspathway()
                                throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLED' property value to an anonymous node

Returns:
pathway, the created value
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

setCONTROLLED_aspathway

pathway setCONTROLLED_aspathway(com.hp.hpl.jena.rdf.model.Resource resource)
                                throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties. This method is equivalent constructing a new instance of pathway with the factory. and calling setCONTROLLED(fr.curie.BiNoM.pathways.biopax.pathway CONTROLLED) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#pathway. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:
{@link - com.hp.hpl.jena.rdf.model.Resource} must not be be null.
Returns:
pathway, the newly created value
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROLLEDProperty

getCONTROL_DASH_TYPE

java.lang.String getCONTROL_DASH_TYPE()
                                      throws com.ibm.adtech.jastor.JastorException
Gets the 'CONTROL_DASH_TYPE' property value

Returns:
String
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROL_DASH_TYPEProperty

setCONTROL_DASH_TYPE

void setCONTROL_DASH_TYPE(java.lang.String CONTROL_DASH_TYPE)
                          throws com.ibm.adtech.jastor.JastorException
Sets the 'CONTROL_DASH_TYPE' property value

Parameters:
{@link - java.lang.String}
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
CONTROL_DASH_TYPEProperty
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