fr.curie.BiNoM.pathways.biopax
Interface evidence

All Superinterfaces:

com.ibm.adtech.jastor.Thing, utilityClass

All Known Implementing Classes:

evidenceImpl

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

Interface for evidence 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#evidence)

RDF Schema Standard Properties
comment : Definition: The support for a particular assertion, such as the existence of an interaction or pathway. At least one of CONFIDENCE, EVIDENCE-CODE, or EXPERIMENTAL-FORM must be instantiated when creating an evidence instance. XREF may reference a publication describing the experimental evidence using a publicationXref or may store a description of the experiment in an experimental description database using a unificationXref (if the referenced experiment is the same) or relationshipXref (if it is not identical, but similar in some way e.g. similar in protocol). Evidence is meant to provide more information than just an xref to the source paper. Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	CONFIDENCEProperty The Jena Property for CONFIDENCE
static com.hp.hpl.jena.rdf.model.Property	EVIDENCE_DASH_CODEProperty The Jena Property for EVIDENCE_DASH_CODE
static com.hp.hpl.jena.rdf.model.Property	EXPERIMENTAL_DASH_FORMProperty The Jena Property for EXPERIMENTAL_DASH_FORM
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

confidence	addCONFIDENCE() Adds an anonymous value for the 'CONFIDENCE' property
void	addCONFIDENCE(confidence CONFIDENCE) Adds a value for the 'CONFIDENCE' property
confidence	addCONFIDENCE(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'CONFIDENCE' property.
openControlledVocabulary	addEVIDENCE_DASH_CODE() Adds an anonymous value for the 'EVIDENCE_DASH_CODE' property
void	addEVIDENCE_DASH_CODE(openControlledVocabulary EVIDENCE_DASH_CODE) Adds a value for the 'EVIDENCE_DASH_CODE' property
openControlledVocabulary	addEVIDENCE_DASH_CODE(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'EVIDENCE_DASH_CODE' property.
experimentalForm	addEXPERIMENTAL_DASH_FORM() Adds an anonymous value for the 'EXPERIMENTAL_DASH_FORM' property
void	addEXPERIMENTAL_DASH_FORM(experimentalForm EXPERIMENTAL_DASH_FORM) Adds a value for the 'EXPERIMENTAL_DASH_FORM' property
experimentalForm	addEXPERIMENTAL_DASH_FORM(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'EXPERIMENTAL_DASH_FORM' 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(xref XREF) Adds a value for the 'XREF' property
java.util.Iterator	getCONFIDENCE() Get an Iterator the 'CONFIDENCE' property values.
java.util.Iterator	getEVIDENCE_DASH_CODE() Get an Iterator the 'EVIDENCE_DASH_CODE' property values.
java.util.Iterator	getEXPERIMENTAL_DASH_FORM() Get an Iterator the 'EXPERIMENTAL_DASH_FORM' property values.
java.util.Iterator	getXREF() Get an Iterator the 'XREF' property values.
void	removeCONFIDENCE(confidence CONFIDENCE) Removes a value for the 'CONFIDENCE' property.
void	removeEVIDENCE_DASH_CODE(openControlledVocabulary EVIDENCE_DASH_CODE) Removes a value for the 'EVIDENCE_DASH_CODE' property.
void	removeEXPERIMENTAL_DASH_FORM(experimentalForm EXPERIMENTAL_DASH_FORM) Removes a value for the 'EXPERIMENTAL_DASH_FORM' 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

EXPERIMENTAL_DASH_FORMProperty

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

The Jena Property for EXPERIMENTAL_DASH_FORM

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

RDF Schema Standard Properties
comment : The experimental forms associated with an evidence instance.^^http://www.w3.org/2001/XMLSchema#string

EVIDENCE_DASH_CODEProperty

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

The Jena Property for EVIDENCE_DASH_CODE

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

RDF Schema Standard Properties
comment : A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.^^http://www.w3.org/2001/XMLSchema#string

CONFIDENCEProperty

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

The Jena Property for CONFIDENCE

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

RDF Schema Standard Properties
comment : Confidence in the containing instance. Usually a statistical measure.^^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

getEXPERIMENTAL_DASH_FORM

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

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

Returns:

Iterator of experimentalForm

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EXPERIMENTAL_DASH_FORMProperty

addEXPERIMENTAL_DASH_FORM

void addEXPERIMENTAL_DASH_FORM(experimentalForm EXPERIMENTAL_DASH_FORM)
                               throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'EXPERIMENTAL_DASH_FORM' property

Parameters:

The - experimentalForm to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EXPERIMENTAL_DASH_FORMProperty

addEXPERIMENTAL_DASH_FORM

experimentalForm addEXPERIMENTAL_DASH_FORM()
                                           throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'EXPERIMENTAL_DASH_FORM' property

Returns:

The anoymous experimentalForm created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EXPERIMENTAL_DASH_FORMProperty

addEXPERIMENTAL_DASH_FORM

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

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

EXPERIMENTAL_DASH_FORMProperty

removeEXPERIMENTAL_DASH_FORM

void removeEXPERIMENTAL_DASH_FORM(experimentalForm EXPERIMENTAL_DASH_FORM)
                                  throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'EXPERIMENTAL_DASH_FORM' 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 - experimentalForm to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EXPERIMENTAL_DASH_FORMProperty

getEVIDENCE_DASH_CODE

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

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

Returns:

Iterator of openControlledVocabulary

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCE_DASH_CODEProperty

addEVIDENCE_DASH_CODE

void addEVIDENCE_DASH_CODE(openControlledVocabulary EVIDENCE_DASH_CODE)
                           throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'EVIDENCE_DASH_CODE' property

Parameters:

The - openControlledVocabulary to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCE_DASH_CODEProperty

addEVIDENCE_DASH_CODE

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

Adds an anonymous value for the 'EVIDENCE_DASH_CODE' property

Returns:

The anoymous openControlledVocabulary created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCE_DASH_CODEProperty

addEVIDENCE_DASH_CODE

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

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

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCE_DASH_CODEProperty

removeEVIDENCE_DASH_CODE

void removeEVIDENCE_DASH_CODE(openControlledVocabulary EVIDENCE_DASH_CODE)
                              throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'EVIDENCE_DASH_CODE' 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 - openControlledVocabulary to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EVIDENCE_DASH_CODEProperty

getCONFIDENCE

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

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

Returns:

Iterator of confidence

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CONFIDENCEProperty

addCONFIDENCE

void addCONFIDENCE(confidence CONFIDENCE)
                   throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'CONFIDENCE' property

Parameters:

The - confidence to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CONFIDENCEProperty

addCONFIDENCE

confidence addCONFIDENCE()
                         throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'CONFIDENCE' property

Returns:

The anoymous confidence created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CONFIDENCEProperty

addCONFIDENCE

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

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

CONFIDENCEProperty

removeCONFIDENCE

void removeCONFIDENCE(confidence CONFIDENCE)
                      throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'CONFIDENCE' 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 - confidence to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

CONFIDENCEProperty

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