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fr.curie.BiNoM.pathways.biopax
Interface entity

All Superinterfaces:
com.ibm.adtech.jastor.Thing
All Known Subinterfaces:
biochemicalReaction, catalysis, complex, complexAssembly, control, conversion, dna, interaction, modulation, pathway, physicalEntity, physicalInteraction, protein, rna, smallMolecule, transport, transportWithBiochemicalReaction
All Known Implementing Classes:
biochemicalReactionImpl, catalysisImpl, complexAssemblyImpl, complexImpl, controlImpl, conversionImpl, dnaImpl, entityImpl, interactionImpl, modulationImpl, pathwayImpl, physicalEntityImpl, physicalInteractionImpl, proteinImpl, rnaImpl, smallMoleculeImpl, transportImpl, transportWithBiochemicalReactionImpl
public interface entity
extends com.ibm.adtech.jastor.Thing

Interface for entity 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#entity)


RDF Schema Standard Properties
comment : Definition: A discrete biological unit used when describing pathways. Comment: This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. As the most abstract class in the ontology, instances of the entity class should never be created. Instead, more specific classes should be used. Synonyms: thing, object, bioentity.^^http://www.w3.org/2001/XMLSchema#string


Field Summary
static com.hp.hpl.jena.rdf.model.Property AVAILABILITYProperty
          The Jena Property for AVAILABILITY
static com.hp.hpl.jena.rdf.model.Property COMMENTProperty
          The Jena Property for COMMENT
static com.hp.hpl.jena.rdf.model.Property DATA_DASH_SOURCEProperty
          The Jena Property for DATA_DASH_SOURCE
static com.hp.hpl.jena.rdf.model.Property NAMEProperty
          The Jena Property for NAME
static com.hp.hpl.jena.rdf.model.Property SHORT_DASH_NAMEProperty
          The Jena Property for SHORT_DASH_NAME
static com.hp.hpl.jena.rdf.model.Property SYNONYMSProperty
          The Jena Property for SYNONYMS
static com.hp.hpl.jena.rdf.model.Resource TYPE
          The rdf:type for this ontology class
static com.hp.hpl.jena.rdf.model.Property XREFProperty
          The Jena Property for XREF
 
Fields inherited from interface com.ibm.adtech.jastor.Thing
copyright
 
Method Summary
 void addAVAILABILITY(java.lang.String AVAILABILITY)
          Add a 'AVAILABILITY' property value
 void addCOMMENT(java.lang.String COMMENT)
          Add a 'COMMENT' property value
 dataSource addDATA_DASH_SOURCE()
          Adds an anonymous value for the 'DATA_DASH_SOURCE' property
 void addDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE)
          Adds a value for the 'DATA_DASH_SOURCE' property
 dataSource addDATA_DASH_SOURCE(com.hp.hpl.jena.rdf.model.Resource resource)
          Adds a value for the 'DATA_DASH_SOURCE' property.
 void addSYNONYMS(java.lang.String SYNONYMS)
          Add a 'SYNONYMS' property value
 xref addXREF()
          Adds an anonymous value for the 'XREF' property
 xref addXREF(com.hp.hpl.jena.rdf.model.Resource resource)
          Adds a value for the 'XREF' property.
 void addXREF(xref XREF)
          Adds a value for the 'XREF' property
 java.util.Iterator getAVAILABILITY()
          Iterates through the 'AVAILABILITY' property values.
 java.util.Iterator getCOMMENT()
          Iterates through the 'COMMENT' property values.
 java.util.Iterator getDATA_DASH_SOURCE()
          Get an Iterator the 'DATA_DASH_SOURCE' property values.
 java.lang.String getNAME()
          Gets the 'NAME' property value
 java.lang.String getSHORT_DASH_NAME()
          Gets the 'SHORT_DASH_NAME' property value
 java.util.Iterator getSYNONYMS()
          Iterates through the 'SYNONYMS' property values.
 java.util.Iterator getXREF()
          Get an Iterator the 'XREF' property values.
 void removeAVAILABILITY(java.lang.String AVAILABILITY)
          Remove a 'AVAILABILITY' property value.
 void removeCOMMENT(java.lang.String COMMENT)
          Remove a 'COMMENT' property value.
 void removeDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE)
          Removes a value for the 'DATA_DASH_SOURCE' property.
 void removeSYNONYMS(java.lang.String SYNONYMS)
          Remove a 'SYNONYMS' property value.
 void removeXREF(xref XREF)
          Removes a value for the 'XREF' property.
 void setNAME(java.lang.String NAME)
          Sets the 'NAME' property value
 void setSHORT_DASH_NAME(java.lang.String SHORT_DASH_NAME)
          Sets the 'SHORT_DASH_NAME' property value
 
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

DATA_DASH_SOURCEProperty

static final com.hp.hpl.jena.rdf.model.Property DATA_DASH_SOURCEProperty
The Jena Property for DATA_DASH_SOURCE

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



RDF Schema Standard Properties
comment : A free text description of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation.^^http://www.w3.org/2001/XMLSchema#string

AVAILABILITYProperty

static final com.hp.hpl.jena.rdf.model.Property AVAILABILITYProperty
The Jena Property for AVAILABILITY

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



RDF Schema Standard Properties
comment : Describes the availability of this data (e.g. a copyright statement).@en

COMMENTProperty

static final com.hp.hpl.jena.rdf.model.Property COMMENTProperty
The Jena Property for COMMENT

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



RDF Schema Standard Properties
comment : Comment on the data in the container class. This property should be used instead of the OWL documentation elements (rdfs:comment) for instances because information in COMMENT is data to be exchanged, whereas the rdfs:comment field is used for metadata about the structure of the BioPAX ontology.^^http://www.w3.org/2001/XMLSchema#string

SHORT_DASH_NAMEProperty

static final com.hp.hpl.jena.rdf.model.Property SHORT_DASH_NAMEProperty
The Jena Property for SHORT_DASH_NAME

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



RDF Schema Standard Properties
comment : An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.^^http://www.w3.org/2001/XMLSchema#string

SYNONYMSProperty

static final com.hp.hpl.jena.rdf.model.Property SYNONYMSProperty
The Jena Property for SYNONYMS

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



RDF Schema Standard Properties
comment : One or more synonyms for the name of this entity. This should include the values of the NAME and SHORT-NAME property so that it is easy to find all known names in one place.@en

NAMEProperty

static final com.hp.hpl.jena.rdf.model.Property NAMEProperty
The Jena Property for NAME

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



RDF Schema Standard Properties
comment : The preferred full name for this entity.@en

XREFProperty

static final com.hp.hpl.jena.rdf.model.Property XREFProperty
The Jena Property for XREF

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



RDF Schema Standard Properties
comment : Values of this property define external cross-references from this entity to entities in external databases.@en

Method Detail

getDATA_DASH_SOURCE

java.util.Iterator getDATA_DASH_SOURCE()
                                       throws com.ibm.adtech.jastor.JastorException
Get an Iterator the 'DATA_DASH_SOURCE' property values. This Iteartor may be used to remove all such values.

Returns:
Iterator of dataSource
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
DATA_DASH_SOURCEProperty

addDATA_DASH_SOURCE

void addDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE)
                         throws com.ibm.adtech.jastor.JastorException
Adds a value for the 'DATA_DASH_SOURCE' property

Parameters:
The - dataSource to add
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
DATA_DASH_SOURCEProperty

addDATA_DASH_SOURCE

dataSource addDATA_DASH_SOURCE()
                               throws com.ibm.adtech.jastor.JastorException
Adds an anonymous value for the 'DATA_DASH_SOURCE' property

Returns:
The anoymous dataSource created
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
DATA_DASH_SOURCEProperty

addDATA_DASH_SOURCE

dataSource addDATA_DASH_SOURCE(com.hp.hpl.jena.rdf.model.Resource resource)
                               throws com.ibm.adtech.jastor.JastorException
Adds a value for the 'DATA_DASH_SOURCE' property. This method is equivalent constructing a new instance of dataSource with the factory and calling addDATA_DASH_SOURCE(fr.curie.BiNoM.pathways.biopax.dataSource DATA_DASH_SOURCE) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#dataSource. 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:
DATA_DASH_SOURCEProperty

removeDATA_DASH_SOURCE

void removeDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE)
                            throws com.ibm.adtech.jastor.JastorException
Removes a value for the 'DATA_DASH_SOURCE' 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 - dataSource to remove
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
DATA_DASH_SOURCEProperty

getAVAILABILITY

java.util.Iterator getAVAILABILITY()
                                   throws com.ibm.adtech.jastor.JastorException
Iterates through the 'AVAILABILITY' property values. This Iteartor may be used to remove all such values.

Returns:
Iterator of String
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
AVAILABILITYProperty

addAVAILABILITY

void addAVAILABILITY(java.lang.String AVAILABILITY)
                     throws com.ibm.adtech.jastor.JastorException
Add a 'AVAILABILITY' property value

Parameters:
{@link - java.lang.String}, the value to add
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
AVAILABILITYProperty

removeAVAILABILITY

void removeAVAILABILITY(java.lang.String AVAILABILITY)
                        throws com.ibm.adtech.jastor.JastorException
Remove a 'AVAILABILITY' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:
{@link - java.lang.String}, the value to remove
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
AVAILABILITYProperty

getCOMMENT

java.util.Iterator getCOMMENT()
                              throws com.ibm.adtech.jastor.JastorException
Iterates through the 'COMMENT' property values. This Iteartor may be used to remove all such values.

Returns:
Iterator of String
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
COMMENTProperty

addCOMMENT

void addCOMMENT(java.lang.String COMMENT)
                throws com.ibm.adtech.jastor.JastorException
Add a 'COMMENT' property value

Parameters:
{@link - java.lang.String}, the value to add
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
COMMENTProperty

removeCOMMENT

void removeCOMMENT(java.lang.String COMMENT)
                   throws com.ibm.adtech.jastor.JastorException
Remove a 'COMMENT' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:
{@link - java.lang.String}, the value to remove
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
COMMENTProperty

getSHORT_DASH_NAME

java.lang.String getSHORT_DASH_NAME()
                                    throws com.ibm.adtech.jastor.JastorException
Gets the 'SHORT_DASH_NAME' property value

Returns:
String
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
SHORT_DASH_NAMEProperty

setSHORT_DASH_NAME

void setSHORT_DASH_NAME(java.lang.String SHORT_DASH_NAME)
                        throws com.ibm.adtech.jastor.JastorException
Sets the 'SHORT_DASH_NAME' property value

Parameters:
{@link - java.lang.String}
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
SHORT_DASH_NAMEProperty

getSYNONYMS

java.util.Iterator getSYNONYMS()
                               throws com.ibm.adtech.jastor.JastorException
Iterates through the 'SYNONYMS' property values. This Iteartor may be used to remove all such values.

Returns:
Iterator of String
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
SYNONYMSProperty

addSYNONYMS

void addSYNONYMS(java.lang.String SYNONYMS)
                 throws com.ibm.adtech.jastor.JastorException
Add a 'SYNONYMS' property value

Parameters:
{@link - java.lang.String}, the value to add
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
SYNONYMSProperty

removeSYNONYMS

void removeSYNONYMS(java.lang.String SYNONYMS)
                    throws com.ibm.adtech.jastor.JastorException
Remove a 'SYNONYMS' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:
{@link - java.lang.String}, the value to remove
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
SYNONYMSProperty

getNAME

java.lang.String getNAME()
                         throws com.ibm.adtech.jastor.JastorException
Gets the 'NAME' property value

Returns:
String
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
NAMEProperty

setNAME

void setNAME(java.lang.String NAME)
             throws com.ibm.adtech.jastor.JastorException
Sets the 'NAME' property value

Parameters:
{@link - java.lang.String}
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
NAMEProperty

getXREF

java.util.Iterator getXREF()
                           throws com.ibm.adtech.jastor.JastorException
Get an Iterator the 'XREF' property values. This Iteartor may be used to remove all such values.

Returns:
Iterator of xref
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
XREFProperty

addXREF

void addXREF(xref XREF)
             throws com.ibm.adtech.jastor.JastorException
Adds a value for the 'XREF' property

Parameters:
The - xref to add
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
XREFProperty

addXREF

xref addXREF()
             throws com.ibm.adtech.jastor.JastorException
Adds an anonymous value for the 'XREF' property

Returns:
The anoymous xref created
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
XREFProperty

addXREF

xref addXREF(com.hp.hpl.jena.rdf.model.Resource resource)
             throws com.ibm.adtech.jastor.JastorException
Adds a value for the 'XREF' property. This method is equivalent constructing a new instance of xref with the factory and calling addXREF(fr.curie.BiNoM.pathways.biopax.xref XREF) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#xref. 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:
XREFProperty

removeXREF

void removeXREF(xref XREF)
                throws com.ibm.adtech.jastor.JastorException
Removes a value for the 'XREF' 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 - xref to remove
Throws:
com.ibm.adtech.jastor.JastorException
See Also:
XREFProperty
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