fr.curie.BiNoM.pathways.biopax
Interface openControlledVocabulary

All Superinterfaces:

externalReferenceUtilityClass, com.ibm.adtech.jastor.Thing, utilityClass

All Known Implementing Classes:

openControlledVocabularyImpl

public interface openControlledVocabulary
extends externalReferenceUtilityClass, com.ibm.adtech.jastor.Thing

Interface for openControlledVocabulary 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#openControlledVocabulary)

RDF Schema Standard Properties
comment : Definition: Used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO) or other open biological CVs listed on the OBO website (http://obo.sourceforge.net/). Comment: The ID property in unification xrefs to GO and other OBO ontologies should include the ontology name in the ID property (e.g. ID="GO:0005634" instead of ID="0005634").^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	TERMProperty The Jena Property for TERM
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 fr.curie.BiNoM.pathways.biopax.utilityClass

COMMENTProperty

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

copyright

Method Summary

void	addTERM(java.lang.String TERM) Add a 'TERM' property value
unificationXref	addXREF_asunificationXref() Adds an anonymous value for the 'XREF' property
unificationXref	addXREF_asunificationXref(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'XREF' property.
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(unificationXref XREF) Adds a value for the 'XREF' property
void	addXREF(xref XREF) Adds a value for the 'XREF' property
java.util.Iterator	getTERM() Iterates through the 'TERM' property values.
java.util.Iterator	getXREF_asunificationXref() Get an Iterator the 'XREF' property values.
java.util.Iterator	getXREF() Get an Iterator the 'XREF' property values.
void	removeTERM(java.lang.String TERM) Remove a 'TERM' property value.
void	removeXREF(unificationXref XREF) Removes a value for the 'XREF' property.
void	removeXREF(xref XREF) Removes a value for the 'XREF' property.

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

TERMProperty

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

The Jena Property for TERM

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

RDF Schema Standard Properties
comment : The external controlled vocabulary term.^^http://www.w3.org/2001/XMLSchema#string

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

getTERM

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

Iterates through the 'TERM' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

TERMProperty

addTERM

void addTERM(java.lang.String TERM)
             throws com.ibm.adtech.jastor.JastorException

Add a 'TERM' property value

Parameters:

{@link - java.lang.String}, the value to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

TERMProperty

removeTERM

void removeTERM(java.lang.String TERM)
                throws com.ibm.adtech.jastor.JastorException

Remove a 'TERM' 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:

TERMProperty

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

getXREF_asunificationXref

java.util.Iterator getXREF_asunificationXref()
                                             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 unificationXref

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty

addXREF

void addXREF(unificationXref XREF)
             throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'XREF' property

Parameters:

The - unificationXref to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty

addXREF_asunificationXref

unificationXref addXREF_asunificationXref()
                                          throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'XREF' property

Returns:

The anoymous unificationXref created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty

addXREF_asunificationXref

unificationXref addXREF_asunificationXref(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 unificationXref with the factory and calling addXREF(fr.curie.BiNoM.pathways.biopax.unificationXref XREF) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#unificationXref. 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(unificationXref 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 - unificationXref to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

XREFProperty