org.biopax.paxtools.model.level3
Interface ProteinReference

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, EntityReference, Level3Element, Named, Observable, SequenceEntityReference, java.io.Serializable, UtilityClass, XReferrable

All Known Implementing Classes:

ProteinReferenceImpl

public interface ProteinReference
extends SequenceEntityReference

Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence. Members can differ in any combination of cellular location, sequence features and bound partners.

Rationale: Protein molecules, encoded by the same genetic sequence can be present in (combinatorially many) different states, as a result of post translational modifications and non-covalent bonds. Each state, chemically, is a different pool of molecules. They are, however, related to each other because:

• They all share the same "base" genetic sequence.
• They can only be converted to each other but not to any other protein

Comments:Most Protein databases, including UniProt would map one to one with ProteinReferences in BioPAX.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Methods inherited from interface org.biopax.paxtools.model.level3.SequenceEntityReference

getOrganism, getSequence, setOrganism, setSequence

Methods inherited from interface org.biopax.paxtools.model.level3.EntityReference

addEntityFeature, addEntityReferenceType, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getMemberEntityReference, getMemberEntityReferenceOf, removeEntityFeature, removeEntityReferenceType, removeMemberEntityReference

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence