fr.curie.BiNoM.pathways.biopax
Interface physicalEntityParticipant

All Superinterfaces:

com.ibm.adtech.jastor.Thing, utilityClass

All Known Subinterfaces:

sequenceParticipant

All Known Implementing Classes:

physicalEntityParticipantImpl, sequenceParticipantImpl

public interface physicalEntityParticipant
extends utilityClass, com.ibm.adtech.jastor.Thing

Interface for physicalEntityParticipant 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#physicalEntityParticipant)

RDF Schema Standard Properties
comment : Definition: Any additional special characteristics of a physical entity in the context of an interaction. These currently include stoichiometric coefficient and cellular location, but this list may be expanded in later levels. Comment: PhysicalEntityParticipants should not be used in multiple interaction or complex instances. Instead, each interaction and complex should reference its own unique set of physicalEntityParticipants. The reason for this is that a user may add new information about a physicalEntityParticipant for one interaction or complex, such as the presence of a previously unknown post-translational modification, and unwittingly invalidate the physicalEntityParticipant for the other interactions or complexes that make use of it. Example: In the interaction describing the transport of L-arginine into the cytoplasm in E. coli, the LEFT property in the interaction would be filled with an instance of physicalEntityParticipant that specified the location of L-arginine as periplasm and the stoichiometric coefficient as one.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	CELLULAR_DASH_LOCATIONProperty The Jena Property for CELLULAR_DASH_LOCATION
static com.hp.hpl.jena.rdf.model.Property	PHYSICAL_DASH_ENTITYProperty The Jena Property for PHYSICAL_DASH_ENTITY
static com.hp.hpl.jena.rdf.model.Property	STOICHIOMETRIC_DASH_COEFFICIENTProperty The Jena Property for STOICHIOMETRIC_DASH_COEFFICIENT
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.utilityClass

COMMENTProperty

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

copyright

Method Summary

openControlledVocabulary	getCELLULAR_DASH_LOCATION() Gets the 'CELLULAR_DASH_LOCATION' property value
physicalEntity	getPHYSICAL_DASH_ENTITY() Gets the 'PHYSICAL_DASH_ENTITY' property value
java.lang.Double	getSTOICHIOMETRIC_DASH_COEFFICIENT() Gets the 'STOICHIOMETRIC_DASH_COEFFICIENT' property value
openControlledVocabulary	setCELLULAR_DASH_LOCATION() Sets the 'CELLULAR_DASH_LOCATION' property value to an anonymous node
void	setCELLULAR_DASH_LOCATION(openControlledVocabulary CELLULAR_DASH_LOCATION) Sets the 'CELLULAR_DASH_LOCATION' property value
openControlledVocabulary	setCELLULAR_DASH_LOCATION(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'CELLULAR_DASH_LOCATION' property value to the given resource, and add's rdf:type properties.
physicalEntity	setPHYSICAL_DASH_ENTITY() Sets the 'PHYSICAL_DASH_ENTITY' property value to an anonymous node
void	setPHYSICAL_DASH_ENTITY(physicalEntity PHYSICAL_DASH_ENTITY) Sets the 'PHYSICAL_DASH_ENTITY' property value
physicalEntity	setPHYSICAL_DASH_ENTITY(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'PHYSICAL_DASH_ENTITY' property value to the given resource, and add's rdf:type properties.
void	setSTOICHIOMETRIC_DASH_COEFFICIENT(java.lang.Double STOICHIOMETRIC_DASH_COEFFICIENT) Sets the 'STOICHIOMETRIC_DASH_COEFFICIENT' property value

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

addCOMMENT, getCOMMENT, removeCOMMENT

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

PHYSICAL_DASH_ENTITYProperty

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

The Jena Property for PHYSICAL_DASH_ENTITY

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

RDF Schema Standard Properties
comment : The physical entity annotated with stoichiometry and cellular location attributes from the physicalEntityParticipant instance.@en

STOICHIOMETRIC_DASH_COEFFICIENTProperty

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

The Jena Property for STOICHIOMETRIC_DASH_COEFFICIENT

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

RDF Schema Standard Properties
comment : Each value of this property represents the stoichiometric coefficient for one of the physical entities in an interaction or complex. For a given interaction, the stoichiometry should always be used where possible instead of representing the number of participants with separate instances of each participant. If there are three ATP molecules, one ATP molecule should be represented as a participant and the stoichiometry should be set to 3.^^http://www.w3.org/2001/XMLSchema#string

CELLULAR_DASH_LOCATIONProperty

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

The Jena Property for CELLULAR_DASH_LOCATION

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

RDF Schema Standard Properties
comment : A cellular location, e.g. 'cytoplasm'. This should reference a term in the Gene Ontology Cellular Component ontology. The location referred to by this property should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntityParticipants) must be created for each different location. Note: If a location is unknown then the GO term for 'cellular component unknown' (GO:0008372) should be used in the LOCATION property. If the location of a participant in a complex is unspecified, it may be assumed to be the same location as that of the complex. In case of conflicting information, the location of the most outer layer of any nesting should be considered correct. Note: Cellular location describes a specific location of a physical entity as it would be used in e.g. a transport reaction. It does not describe all of the possible locations that the physical entity could be in the cell.^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getPHYSICAL_DASH_ENTITY

physicalEntity getPHYSICAL_DASH_ENTITY()
                                       throws com.ibm.adtech.jastor.JastorException

Gets the 'PHYSICAL_DASH_ENTITY' property value

Returns:

physicalEntity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PHYSICAL_DASH_ENTITYProperty

setPHYSICAL_DASH_ENTITY

void setPHYSICAL_DASH_ENTITY(physicalEntity PHYSICAL_DASH_ENTITY)
                             throws com.ibm.adtech.jastor.JastorException

Sets the 'PHYSICAL_DASH_ENTITY' property value

Parameters:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PHYSICAL_DASH_ENTITYProperty

setPHYSICAL_DASH_ENTITY

physicalEntity setPHYSICAL_DASH_ENTITY()
                                       throws com.ibm.adtech.jastor.JastorException

Sets the 'PHYSICAL_DASH_ENTITY' property value to an anonymous node

Returns:

physicalEntity, the created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PHYSICAL_DASH_ENTITYProperty

setPHYSICAL_DASH_ENTITY

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

Sets the 'PHYSICAL_DASH_ENTITY' property value to the given resource, and add's rdf:type properties. This method is equivalent constructing a new instance of physicalEntity with the factory. and calling setPHYSICAL_DASH_ENTITY(fr.curie.BiNoM.pathways.biopax.physicalEntity PHYSICAL_DASH_ENTITY) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#physicalEntity. 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:

physicalEntity, the newly created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PHYSICAL_DASH_ENTITYProperty

getSTOICHIOMETRIC_DASH_COEFFICIENT

java.lang.Double getSTOICHIOMETRIC_DASH_COEFFICIENT()
                                                    throws com.ibm.adtech.jastor.JastorException

Gets the 'STOICHIOMETRIC_DASH_COEFFICIENT' property value

Returns:

Double

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STOICHIOMETRIC_DASH_COEFFICIENTProperty

setSTOICHIOMETRIC_DASH_COEFFICIENT

void setSTOICHIOMETRIC_DASH_COEFFICIENT(java.lang.Double STOICHIOMETRIC_DASH_COEFFICIENT)
                                        throws com.ibm.adtech.jastor.JastorException

Sets the 'STOICHIOMETRIC_DASH_COEFFICIENT' property value

Parameters:

{@link - java.lang.Double}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

STOICHIOMETRIC_DASH_COEFFICIENTProperty

getCELLULAR_DASH_LOCATION

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

Gets the 'CELLULAR_DASH_LOCATION' property value

Returns:

openControlledVocabulary

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CELLULAR_DASH_LOCATIONProperty

setCELLULAR_DASH_LOCATION

void setCELLULAR_DASH_LOCATION(openControlledVocabulary CELLULAR_DASH_LOCATION)
                               throws com.ibm.adtech.jastor.JastorException

Sets the 'CELLULAR_DASH_LOCATION' property value

Parameters:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CELLULAR_DASH_LOCATIONProperty

setCELLULAR_DASH_LOCATION

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

Sets the 'CELLULAR_DASH_LOCATION' property value to an anonymous node

Returns:

openControlledVocabulary, the created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CELLULAR_DASH_LOCATIONProperty

setCELLULAR_DASH_LOCATION

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

Sets the 'CELLULAR_DASH_LOCATION' property value to the given resource, and add's rdf:type properties. This method is equivalent constructing a new instance of openControlledVocabulary with the factory. and calling setCELLULAR_DASH_LOCATION(fr.curie.BiNoM.pathways.biopax.openControlledVocabulary CELLULAR_DASH_LOCATION) 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:

{@link - com.hp.hpl.jena.rdf.model.Resource} must not be be null.

Returns:

openControlledVocabulary, the newly created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CELLULAR_DASH_LOCATIONProperty