fr.curie.BiNoM.pathways.biopax
Interface physicalInteraction

All Superinterfaces:

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

All Known Subinterfaces:

biochemicalReaction, catalysis, complexAssembly, control, conversion, modulation, transport, transportWithBiochemicalReaction

All Known Implementing Classes:

biochemicalReactionImpl, catalysisImpl, complexAssemblyImpl, controlImpl, conversionImpl, modulationImpl, physicalInteractionImpl, transportImpl, transportWithBiochemicalReactionImpl

public interface physicalInteraction
extends interaction, com.ibm.adtech.jastor.Thing

Interface for physicalInteraction 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#physicalInteraction)

RDF Schema Standard Properties
comment : Definition: An interaction in which at least one participant is a physical entity, e.g. a binding event. Comment: This class should be used by default for representing molecular interactions, such as those defined by PSI-MI level 2. The participants in a molecular interaction should be listed in the PARTICIPANTS slot. Note that this is one of the few cases in which the PARTICPANT slot should be directly populated with instances (see comments on the PARTICPANTS property in the interaction class description). If sufficient information on the nature of a molecular interaction is available, a more specific BioPAX interaction class should be used. Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	INTERACTION_DASH_TYPEProperty The Jena Property for INTERACTION_DASH_TYPE
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.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

openControlledVocabulary	addINTERACTION_DASH_TYPE() Adds an anonymous value for the 'INTERACTION_DASH_TYPE' property
void	addINTERACTION_DASH_TYPE(openControlledVocabulary INTERACTION_DASH_TYPE) Adds a value for the 'INTERACTION_DASH_TYPE' property
openControlledVocabulary	addINTERACTION_DASH_TYPE(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'INTERACTION_DASH_TYPE' property.
physicalEntityParticipant	addPARTICIPANTS_asphysicalEntityParticipant() Adds an anonymous value for the 'PARTICIPANTS' property
physicalEntityParticipant	addPARTICIPANTS_asphysicalEntityParticipant(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PARTICIPANTS' property.
void	addPARTICIPANTS(physicalEntityParticipant PARTICIPANTS) Adds a value for the 'PARTICIPANTS' property
java.util.Iterator	getINTERACTION_DASH_TYPE() Get an Iterator the 'INTERACTION_DASH_TYPE' property values.
java.util.Iterator	getPARTICIPANTS_asphysicalEntityParticipant() Get an Iterator the 'PARTICIPANTS' property values.
void	removeINTERACTION_DASH_TYPE(openControlledVocabulary INTERACTION_DASH_TYPE) Removes a value for the 'INTERACTION_DASH_TYPE' property.
void	removePARTICIPANTS(physicalEntityParticipant PARTICIPANTS) Removes a value for the 'PARTICIPANTS' property.

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

INTERACTION_DASH_TYPEProperty

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

The Jena Property for INTERACTION_DASH_TYPE

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

RDF Schema Standard Properties
comment : External controlled vocabulary characterizing the interaction type, for example "phosphorylation".^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getPARTICIPANTS_asphysicalEntityParticipant

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

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

Specified by:

getPARTICIPANTS_asphysicalEntityParticipant in interface interaction

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

addPARTICIPANTS

void addPARTICIPANTS(physicalEntityParticipant PARTICIPANTS)
                     throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'PARTICIPANTS' property

Specified by:

addPARTICIPANTS in interface interaction

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

addPARTICIPANTS_asphysicalEntityParticipant

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

Adds an anonymous value for the 'PARTICIPANTS' property

Specified by:

addPARTICIPANTS_asphysicalEntityParticipant in interface interaction

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

addPARTICIPANTS_asphysicalEntityParticipant

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

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

Specified by:

addPARTICIPANTS_asphysicalEntityParticipant in interface interaction

Parameters:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

removePARTICIPANTS

void removePARTICIPANTS(physicalEntityParticipant PARTICIPANTS)
                        throws com.ibm.adtech.jastor.JastorException

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

Specified by:

removePARTICIPANTS in interface interaction

Parameters:

The - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

getINTERACTION_DASH_TYPE

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

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

Returns:

Iterator of openControlledVocabulary

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

INTERACTION_DASH_TYPEProperty

addINTERACTION_DASH_TYPE

void addINTERACTION_DASH_TYPE(openControlledVocabulary INTERACTION_DASH_TYPE)
                              throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'INTERACTION_DASH_TYPE' property

Parameters:

The - openControlledVocabulary to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

INTERACTION_DASH_TYPEProperty

addINTERACTION_DASH_TYPE

openControlledVocabulary addINTERACTION_DASH_TYPE()
                                                  throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'INTERACTION_DASH_TYPE' property

Returns:

The anoymous openControlledVocabulary created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

INTERACTION_DASH_TYPEProperty

addINTERACTION_DASH_TYPE

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

Adds a value for the 'INTERACTION_DASH_TYPE' property. This method is equivalent constructing a new instance of openControlledVocabulary with the factory and calling addINTERACTION_DASH_TYPE(fr.curie.BiNoM.pathways.biopax.openControlledVocabulary INTERACTION_DASH_TYPE) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#openControlledVocabulary. 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:

INTERACTION_DASH_TYPEProperty

removeINTERACTION_DASH_TYPE

void removeINTERACTION_DASH_TYPE(openControlledVocabulary INTERACTION_DASH_TYPE)
                                 throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'INTERACTION_DASH_TYPE' 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 - openControlledVocabulary to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

INTERACTION_DASH_TYPEProperty