org.biopax.paxtools.model.level3
Interface SequenceModificationVocabulary

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, ControlledVocabulary, Level3Element, java.io.Serializable, UtilityClass, XReferrable

All Known Implementing Classes:

SequenceModificationVocabularyImpl

public interface SequenceModificationVocabulary
extends ControlledVocabulary

Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain. For proteins this is reference to the PSI Molecular Interaction ontology (MI) of covalent sequence modifications. For nucleic acids, there is currently no recommended standard CV.

Usage: Whenever possible the most specific term in the ontology should be used. For example PSI-MI term o-phospho-serine should be used instead of the parent "phosphorylated residue" when annotating a phosphorylation at a known serine amino acid.

See Also:

PSI Dev, PSI Biological Feature, Candidate RNA modification CV

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.ControlledVocabulary

addTerm, getTerm, removeTerm

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