fr.curie.BiNoM.pathways.biopax
Interface pathway

All Superinterfaces:

entity, com.ibm.adtech.jastor.Thing

All Known Implementing Classes:

pathwayImpl

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

Interface for pathway 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#pathway)

RDF Schema Standard Properties
comment : Definition: A set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical or other reasons. Comment: It is possible to define a pathway without specifying the interactions within the pathway. In this case, the pathway instance could consist simply of a name and could be treated as a 'black box'. Synonyms: network Examples: glycolysis, valine biosynthesis^^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	ORGANISMProperty The Jena Property for ORGANISM
static com.hp.hpl.jena.rdf.model.Property	PATHWAY_DASH_COMPONENTSProperty The Jena Property for PATHWAY_DASH_COMPONENTS
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.
interaction	addPATHWAY_DASH_COMPONENTS_asinteraction() Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property
interaction	addPATHWAY_DASH_COMPONENTS_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.
pathway	addPATHWAY_DASH_COMPONENTS_aspathway() Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property
pathway	addPATHWAY_DASH_COMPONENTS_aspathway(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.
pathwayStep	addPATHWAY_DASH_COMPONENTS_aspathwayStep() Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property
pathwayStep	addPATHWAY_DASH_COMPONENTS_aspathwayStep(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.
void	addPATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property
void	addPATHWAY_DASH_COMPONENTS(pathway PATHWAY_DASH_COMPONENTS) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property
void	addPATHWAY_DASH_COMPONENTS(pathwayStep PATHWAY_DASH_COMPONENTS) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property
java.util.Iterator	getEVIDENCE() Get an Iterator the 'EVIDENCE' property values.
bioSource	getORGANISM() Gets the 'ORGANISM' property value
java.util.Iterator	getPATHWAY_DASH_COMPONENTS_asinteraction() Get an Iterator the 'PATHWAY_DASH_COMPONENTS' property values.
java.util.Iterator	getPATHWAY_DASH_COMPONENTS_aspathway() Get an Iterator the 'PATHWAY_DASH_COMPONENTS' property values.
java.util.Iterator	getPATHWAY_DASH_COMPONENTS_aspathwayStep() Get an Iterator the 'PATHWAY_DASH_COMPONENTS' property values.
void	removeEVIDENCE(evidence EVIDENCE) Removes a value for the 'EVIDENCE' property.
void	removePATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS) Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.
void	removePATHWAY_DASH_COMPONENTS(pathway PATHWAY_DASH_COMPONENTS) Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.
void	removePATHWAY_DASH_COMPONENTS(pathwayStep PATHWAY_DASH_COMPONENTS) Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.
bioSource	setORGANISM() Sets the 'ORGANISM' property value to an anonymous node
void	setORGANISM(bioSource ORGANISM) Sets the 'ORGANISM' property value
bioSource	setORGANISM(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'ORGANISM' property value to the given resource, and add's rdf:type properties.

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

PATHWAY_DASH_COMPONENTSProperty

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

The Jena Property for PATHWAY_DASH_COMPONENTS

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

RDF Schema Standard Properties
comment : The set of interactions and/or pathwaySteps in this pathway/network. Each instance of the pathwayStep class defines: 1) a set of interactions that together define a particular step in the pathway, for example a catalysis instance and the conversion that it catalyzes; 2) an order relationship to one or more other pathway steps (via the NEXT-STEP property). Note: This ordering is not necessarily temporal - the order described may simply represent connectivity between adjacent steps. Temporal ordering information should only be inferred from the direction of each interaction.^^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

ORGANISMProperty

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

The Jena Property for ORGANISM

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

RDF Schema Standard Properties
comment : An organism, e.g. 'Homo sapiens'. This is the organism that the entity is found in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.@en

Method Detail

getPATHWAY_DASH_COMPONENTS_asinteraction

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

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

Returns:

Iterator of interaction

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS

void addPATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS)
                                throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property

Parameters:

The - interaction to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS_asinteraction

interaction addPATHWAY_DASH_COMPONENTS_asinteraction()
                                                     throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property

Returns:

The anoymous interaction created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS_asinteraction

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

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

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

removePATHWAY_DASH_COMPONENTS

void removePATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS)
                                   throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'PATHWAY_DASH_COMPONENTS' 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 - interaction to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

getPATHWAY_DASH_COMPONENTS_aspathwayStep

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

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

Returns:

Iterator of pathwayStep

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS

void addPATHWAY_DASH_COMPONENTS(pathwayStep PATHWAY_DASH_COMPONENTS)
                                throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property

Parameters:

The - pathwayStep to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS_aspathwayStep

pathwayStep addPATHWAY_DASH_COMPONENTS_aspathwayStep()
                                                     throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property

Returns:

The anoymous pathwayStep created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS_aspathwayStep

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

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

PATHWAY_DASH_COMPONENTSProperty

removePATHWAY_DASH_COMPONENTS

void removePATHWAY_DASH_COMPONENTS(pathwayStep PATHWAY_DASH_COMPONENTS)
                                   throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'PATHWAY_DASH_COMPONENTS' 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 - pathwayStep to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

getPATHWAY_DASH_COMPONENTS_aspathway

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

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

Returns:

Iterator of pathway

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS

void addPATHWAY_DASH_COMPONENTS(pathway PATHWAY_DASH_COMPONENTS)
                                throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property

Parameters:

The - pathway to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS_aspathway

pathway addPATHWAY_DASH_COMPONENTS_aspathway()
                                             throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property

Returns:

The anoymous pathway created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

addPATHWAY_DASH_COMPONENTS_aspathway

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

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

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

removePATHWAY_DASH_COMPONENTS

void removePATHWAY_DASH_COMPONENTS(pathway PATHWAY_DASH_COMPONENTS)
                                   throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'PATHWAY_DASH_COMPONENTS' 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 - pathway to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

PATHWAY_DASH_COMPONENTSProperty

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

getORGANISM

bioSource getORGANISM()
                      throws com.ibm.adtech.jastor.JastorException

Gets the 'ORGANISM' property value

Returns:

bioSource

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

setORGANISM

void setORGANISM(bioSource ORGANISM)
                 throws com.ibm.adtech.jastor.JastorException

Sets the 'ORGANISM' property value

Parameters:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

setORGANISM

bioSource setORGANISM()
                      throws com.ibm.adtech.jastor.JastorException

Sets the 'ORGANISM' property value to an anonymous node

Returns:

bioSource, the created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

setORGANISM

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

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

bioSource, the newly created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty