fr.curie.BiNoM.pathways.biopax
Interface interaction

All Superinterfaces:

entity, com.ibm.adtech.jastor.Thing

All Known Subinterfaces:

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

All Known Implementing Classes:

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

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

Interface for interaction 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#interaction)

RDF Schema Standard Properties
comment : Definition: A single biological relationship between two or more entities. An interaction cannot be defined without the entities it relates. Comment: Since it is a highly abstract class in the ontology, instances of the interaction class should never be created. Instead, more specific classes should be used. Currently this class only has subclasses that define physical interactions; later levels of BioPAX may define other types of interactions, such as genetic (e.g. synthetic lethal). Naming rationale: A number of names were considered for this concept, including "process", "synthesis" and "relationship"; Interaction was chosen as it is understood by biologists in a biological context and is compatible with PSI-MI. Examples: protein-protein interaction, biochemical reaction, enzyme catalysis^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	EVIDENCEProperty The Jena Property for EVIDENCE
static com.hp.hpl.jena.rdf.model.Property	PARTICIPANTSProperty The Jena Property for PARTICIPANTS
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.entity

AVAILABILITYProperty, COMMENTProperty, DATA_DASH_SOURCEProperty, NAMEProperty, SHORT_DASH_NAMEProperty, SYNONYMSProperty, XREFProperty

Fields inherited from interface com.ibm.adtech.jastor.Thing

copyright

Method Summary

evidence	addEVIDENCE() Adds an anonymous value for the 'EVIDENCE' property
void	addEVIDENCE(evidence EVIDENCE) Adds a value for the 'EVIDENCE' property
evidence	addEVIDENCE(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'EVIDENCE' property.
entity	addPARTICIPANTS_asentity() Adds an anonymous value for the 'PARTICIPANTS' property
entity	addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PARTICIPANTS' 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(entity PARTICIPANTS) Adds a value for the 'PARTICIPANTS' property
void	addPARTICIPANTS(physicalEntityParticipant PARTICIPANTS) Adds a value for the 'PARTICIPANTS' property
java.util.Iterator	getEVIDENCE() Get an Iterator the 'EVIDENCE' property values.
java.util.Iterator	getPARTICIPANTS_asentity() Get an Iterator the 'PARTICIPANTS' property values.
java.util.Iterator	getPARTICIPANTS_asphysicalEntityParticipant() Get an Iterator the 'PARTICIPANTS' property values.
void	removeEVIDENCE(evidence EVIDENCE) Removes a value for the 'EVIDENCE' property.
void	removePARTICIPANTS(entity PARTICIPANTS) Removes a value for the 'PARTICIPANTS' property.
void	removePARTICIPANTS(physicalEntityParticipant PARTICIPANTS) Removes a value for the 'PARTICIPANTS' property.

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

PARTICIPANTSProperty

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

The Jena Property for PARTICIPANTS

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

RDF Schema Standard Properties
comment : This property lists the entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. This property has a number of sub-properties, such as LEFT and RIGHT in the biochemicalInteraction class. Any participant listed in a sub-property will automatically be assumed to also be in PARTICIPANTS by a number of software systems, including Protégé, so this property should not contain any instances if there are instances contained in a sub-property.^^http://www.w3.org/2001/XMLSchema#string

EVIDENCEProperty

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

The Jena Property for EVIDENCE

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

RDF Schema Standard Properties
comment : Scientific evidence supporting the existence of the entity as described.^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getPARTICIPANTS_asentity

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

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

Returns:

Iterator of entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

addPARTICIPANTS

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

Adds a value for the 'PARTICIPANTS' property

Parameters:

The - entity to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

addPARTICIPANTS_asentity

entity addPARTICIPANTS_asentity()
                                throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'PARTICIPANTS' property

Returns:

The anoymous entity created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

addPARTICIPANTS_asentity

entity addPARTICIPANTS_asentity(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 entity with the factory and calling addPARTICIPANTS(fr.curie.BiNoM.pathways.biopax.entity PARTICIPANTS) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#entity. 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:

PARTICIPANTSProperty

removePARTICIPANTS

void removePARTICIPANTS(entity 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.

Parameters:

The - entity to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

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.

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

addPARTICIPANTS

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

Adds a value for the 'PARTICIPANTS' property

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

addPARTICIPANTS_asphysicalEntityParticipant

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

Adds an anonymous value for the 'PARTICIPANTS' property

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

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.

Parameters:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

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.

Parameters:

The - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PARTICIPANTSProperty

getEVIDENCE

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

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

Returns:

Iterator of evidence

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCEProperty

addEVIDENCE

void addEVIDENCE(evidence EVIDENCE)
                 throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'EVIDENCE' property

Parameters:

The - evidence to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCEProperty

addEVIDENCE

evidence addEVIDENCE()
                     throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'EVIDENCE' property

Returns:

The anoymous evidence created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCEProperty

addEVIDENCE

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

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

EVIDENCEProperty

removeEVIDENCE

void removeEVIDENCE(evidence EVIDENCE)
                    throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'EVIDENCE' 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 - evidence to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCEProperty