fr.curie.BiNoM.pathways.biopax
Interface catalysis

All Superinterfaces:

control, entity, interaction, physicalInteraction, com.ibm.adtech.jastor.Thing

All Known Implementing Classes:

catalysisImpl

public interface catalysis
extends control, com.ibm.adtech.jastor.Thing

Interface for catalysis 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#catalysis)

RDF Schema Standard Properties
comment : Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. Instances of this class describe a pairing between a catalyzing entity and a catalyzed conversion. Comment: A separate catalysis instance should be created for each different conversion that a physicalEntity may catalyze and for each different physicalEntity that may catalyze a conversion. For example, a bifunctional enzyme that catalyzes two different biochemical reactions would be linked to each of those biochemical reactions by two separate instances of the catalysis class. Also, catalysis reactions from multiple different organisms could be linked to the same generic biochemical reaction (a biochemical reaction is generic if it only includes small molecules). Generally, the enzyme catalyzing a conversion is known and the use of this class is obvious. In the cases where a catalyzed reaction is known to occur but the enzyme is not known, a catalysis instance should be created without a controller specified (i.e. the CONTROLLER property should remain empty). Synonyms: facilitation, acceleration. Examples: The catalysis of a biochemical reaction by an enzyme, the enabling of a transport interaction by a membrane pore complex, and the facilitation of a complex assembly by a scaffold protein. Hexokinase -> (The "Glucose + ATP -> Glucose-6-phosphate +ADP" reaction). A plasma membrane Na+/K+ ATPase is an active transporter (antiport pump) using the energy of ATP to pump Na+ out of the cell and K+ in. Na+ from cytoplasm to extracellular space would be described in a transport instance. K+ from extracellular space to cytoplasm would be described in a transport instance. The ATPase pump would be stored in a catalysis instance controlling each of the above transport instances. A biochemical reaction that does not occur by itself under physiological conditions, but has been observed to occur in the presence of cell extract, likely via one or more unknown enzymes present in the extract, would be stored in the CONTROLLED property, with the CONTROLLER property empty.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	COFACTORProperty The Jena Property for COFACTOR
static com.hp.hpl.jena.rdf.model.Property	DIRECTIONProperty The Jena Property for DIRECTION
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.control

CONTROL_DASH_TYPEProperty, CONTROLLEDProperty, CONTROLLERProperty

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

physicalEntityParticipant	addCOFACTOR() Adds an anonymous value for the 'COFACTOR' property
void	addCOFACTOR(physicalEntityParticipant COFACTOR) Adds a value for the 'COFACTOR' property
physicalEntityParticipant	addCOFACTOR(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'COFACTOR' property.
java.util.Iterator	getCOFACTOR() Get an Iterator the 'COFACTOR' property values.
conversion	getCONTROLLED_asconversion() Gets the 'CONTROLLED' property value
java.lang.String	getDIRECTION() Gets the 'DIRECTION' property value
void	removeCOFACTOR(physicalEntityParticipant COFACTOR) Removes a value for the 'COFACTOR' property.
conversion	setCONTROLLED_asconversion() Sets the 'CONTROLLED' property value to an anonymous node
conversion	setCONTROLLED_asconversion(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(conversion CONTROLLED) Sets the 'CONTROLLED' property value
void	setDIRECTION(java.lang.String DIRECTION) Sets the 'DIRECTION' property value

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.control

getCONTROL_DASH_TYPE, getCONTROLLED_asinteraction, getCONTROLLED_aspathway, getCONTROLLER, setCONTROL_DASH_TYPE, setCONTROLLED_asinteraction, setCONTROLLED_asinteraction, setCONTROLLED_aspathway, setCONTROLLED_aspathway, setCONTROLLED, setCONTROLLED, setCONTROLLER, setCONTROLLER, setCONTROLLER

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

DIRECTIONProperty

static final com.hp.hpl.jena.rdf.model.Property DIRECTIONProperty

The Jena Property for DIRECTION

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

RDF Schema Standard Properties
comment : Specifies the reaction direction of the interaction catalyzed by this instance of the catalysis class. Possible values of this slot are: REVERSIBLE: Interaction occurs in both directions in physiological settings. PHYSIOL-LEFT-TO-RIGHT PHYSIOL-RIGHT-TO-LEFT The interaction occurs in the specified direction in physiological settings, because of several possible factors including the energetics of the reaction, local concentrations of reactants and products, and the regulation of the enzyme or its expression. IRREVERSIBLE-LEFT-TO-RIGHT IRREVERSIBLE-RIGHT-TO-LEFT For all practical purposes, the interactions occurs only in the specified direction in physiological settings, because of chemical properties of the reaction. (This definition from EcoCyc)^^http://www.w3.org/2001/XMLSchema#string

COFACTORProperty

static final com.hp.hpl.jena.rdf.model.Property COFACTORProperty

The Jena Property for COFACTOR

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

RDF Schema Standard Properties
comment : Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. COFACTOR is a sub-property of PARTICIPANTS.@en

Method Detail

getCONTROLLED_asconversion

conversion getCONTROLLED_asconversion()
                                      throws com.ibm.adtech.jastor.JastorException

Gets the 'CONTROLLED' property value

Returns:

conversion

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

control.CONTROLLEDProperty

setCONTROLLED

void setCONTROLLED(conversion CONTROLLED)
                   throws com.ibm.adtech.jastor.JastorException

Sets the 'CONTROLLED' property value

Parameters:

{@link - fr.curie.BiNoM.pathways.biopax.conversion}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

control.CONTROLLEDProperty

setCONTROLLED_asconversion

conversion setCONTROLLED_asconversion()
                                      throws com.ibm.adtech.jastor.JastorException

Sets the 'CONTROLLED' property value to an anonymous node

Returns:

conversion, the created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

control.CONTROLLEDProperty

setCONTROLLED_asconversion

conversion setCONTROLLED_asconversion(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 conversion with the factory. and calling setCONTROLLED(fr.curie.BiNoM.pathways.biopax.conversion CONTROLLED) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#conversion. 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:

conversion, the newly created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

control.CONTROLLEDProperty

getDIRECTION

java.lang.String getDIRECTION()
                              throws com.ibm.adtech.jastor.JastorException

Gets the 'DIRECTION' property value

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DIRECTIONProperty

setDIRECTION

void setDIRECTION(java.lang.String DIRECTION)
                  throws com.ibm.adtech.jastor.JastorException

Sets the 'DIRECTION' property value

Parameters:

{@link - java.lang.String}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DIRECTIONProperty

getCOFACTOR

java.util.Iterator getCOFACTOR()
                               throws com.ibm.adtech.jastor.JastorException

Get an Iterator the 'COFACTOR' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COFACTORProperty

addCOFACTOR

void addCOFACTOR(physicalEntityParticipant COFACTOR)
                 throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'COFACTOR' property

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COFACTORProperty

addCOFACTOR

physicalEntityParticipant addCOFACTOR()
                                      throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'COFACTOR' property

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COFACTORProperty

addCOFACTOR

physicalEntityParticipant addCOFACTOR(com.hp.hpl.jena.rdf.model.Resource resource)
                                      throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'COFACTOR' property. This method is equivalent constructing a new instance of physicalEntityParticipant with the factory and calling addCOFACTOR(fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant COFACTOR) 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:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COFACTORProperty

removeCOFACTOR

void removeCOFACTOR(physicalEntityParticipant COFACTOR)
                    throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'COFACTOR' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

The - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COFACTORProperty