fr.curie.BiNoM.pathways.biopax
Interface complex

All Superinterfaces:

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

All Known Implementing Classes:

complexImpl

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

Interface for complex 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#complex)

RDF Schema Standard Properties
comment : Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g. protein, DNA, or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complexAssembly) and is not itself considered an interaction. Comment: In general, complexes should not be defined recursively so that smaller complexes exist within larger complexes, i.e. a complex should not be a COMPONENT of another complex (see comments on the COMPONENT property). The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding and the topology of the components cannot be described currently, but may be included in future versions of the ontology, depending on community need. Examples: Ribosome, RNA polymerase II. Other examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	COMPONENTSProperty The Jena Property for COMPONENTS
static com.hp.hpl.jena.rdf.model.Property	ORGANISMProperty The Jena Property for ORGANISM
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

physicalEntityParticipant	addCOMPONENTS() Adds an anonymous value for the 'COMPONENTS' property
void	addCOMPONENTS(physicalEntityParticipant COMPONENTS) Adds a value for the 'COMPONENTS' property
physicalEntityParticipant	addCOMPONENTS(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'COMPONENTS' property.
bioSource	addORGANISM() Adds an anonymous value for the 'ORGANISM' property
void	addORGANISM(bioSource ORGANISM) Adds a value for the 'ORGANISM' property
bioSource	addORGANISM(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'ORGANISM' property.
java.util.Iterator	getCOMPONENTS() Get an Iterator the 'COMPONENTS' property values.
java.util.Iterator	getORGANISM() Get an Iterator the 'ORGANISM' property values.
void	removeCOMPONENTS(physicalEntityParticipant COMPONENTS) Removes a value for the 'COMPONENTS' property.
void	removeORGANISM(bioSource ORGANISM) Removes a value for the 'ORGANISM' property.

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

COMPONENTSProperty

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

The Jena Property for COMPONENTS

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

RDF Schema Standard Properties
comment : Defines the physicalEntity subunits of this complex. This property should not contain other complexes, i.e. it should always be a flat representation of the complex. For example, if two protein complexes join to form a single larger complex via a complex assembly interaction, the COMPONENTS of the new complex should be the individual proteins of the smaller complexes, not the two smaller complexes themselves. Exceptions are black-box complexes (i.e. complexes in which the COMPONENTS property is empty), which may be used as COMPONENTS of other complexes because their constituent parts are unknown / unspecified. The reason for keeping complexes flat is to signify that there is no information stored in the way complexes are nested, such as assembly order.@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

getCOMPONENTS

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

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

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COMPONENTSProperty

addCOMPONENTS

void addCOMPONENTS(physicalEntityParticipant COMPONENTS)
                   throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'COMPONENTS' property

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COMPONENTSProperty

addCOMPONENTS

physicalEntityParticipant addCOMPONENTS()
                                        throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'COMPONENTS' property

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COMPONENTSProperty

addCOMPONENTS

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

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

COMPONENTSProperty

removeCOMPONENTS

void removeCOMPONENTS(physicalEntityParticipant COMPONENTS)
                      throws com.ibm.adtech.jastor.JastorException

Removes a value for the '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 - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

COMPONENTSProperty

getORGANISM

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

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

Returns:

Iterator of bioSource

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

addORGANISM

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

Adds a value for the 'ORGANISM' property

Parameters:

The - bioSource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

addORGANISM

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

Adds an anonymous value for the 'ORGANISM' property

Returns:

The anoymous bioSource created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

addORGANISM

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

Adds a value for the 'ORGANISM' property. This method is equivalent constructing a new instance of bioSource with the factory and calling addORGANISM(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:

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

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty

removeORGANISM

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

Removes a value for the 'ORGANISM' 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 - bioSource to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

ORGANISMProperty