fr.curie.BiNoM.pathways.biopax
Interface protein

All Superinterfaces:

entity, physicalEntity, com.ibm.adtech.jastor.Thing

All Known Implementing Classes:

proteinImpl

public interface protein
extends physicalEntity, com.ibm.adtech.jastor.Thing

Interface for protein 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#protein)

RDF Schema Standard Properties
comment : Definition: A physical entity consisting of a sequence of amino acids; a protein monomer; a single polypeptide chain. Examples: The epidermal growth factor receptor (EGFR) protein.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	ORGANISMProperty The Jena Property for ORGANISM
static com.hp.hpl.jena.rdf.model.Property	SEQUENCEProperty The Jena Property for SEQUENCE
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

bioSource	getORGANISM() Gets the 'ORGANISM' property value
java.lang.String	getSEQUENCE() Gets the 'SEQUENCE' property value
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.
void	setSEQUENCE(java.lang.String SEQUENCE) Sets the 'SEQUENCE' property value

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

SEQUENCEProperty

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

The Jena Property for SEQUENCE

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

RDF Schema Standard Properties
comment : Polymer sequence in uppercase letters. For DNA, usually A,C,G,T letters representing the nucleosides of adenine, cytosine, guanine and thymine, respectively; for RNA, usually A, C, U, G; for protein, usually the letters corresponding to the 20 letter IUPAC amino acid code.@en

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

getSEQUENCE

java.lang.String getSEQUENCE()
                             throws com.ibm.adtech.jastor.JastorException

Gets the 'SEQUENCE' property value

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SEQUENCEProperty

setSEQUENCE

void setSEQUENCE(java.lang.String SEQUENCE)
                 throws com.ibm.adtech.jastor.JastorException

Sets the 'SEQUENCE' property value

Parameters:

{@link - java.lang.String}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SEQUENCEProperty

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