Uses of Interface
org.biopax.paxtools.model.level3.Level3Element

Packages that use Level3Element

Package	Description
org.biopax.paxtools.impl.level3	This package contains the default implementation for BioPAX Level 3.
org.biopax.paxtools.model.level3	This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.

Uses of Level3Element in org.biopax.paxtools.impl.level3

Classes in org.biopax.paxtools.impl.level3 that implement Level3Element

Modifier and Type	Class	Description
class	BindingFeatureImpl
class	BiochemicalPathwayStepImpl
class	BiochemicalReactionImpl
class	BioSourceImpl
class	CatalysisImpl
class	CellularLocationVocabularyImpl
class	CellVocabularyImpl
class	ChemicalConstantImpl
class	ChemicalStructureImpl
class	ComplexAssemblyImpl
class	ComplexImpl
class	ControlImpl
class	ControlledVocabularyImpl
class	ConversionImpl
class	CovalentBindingFeatureImpl
class	DegradationImpl
class	DeltaGImpl
class	DnaImpl
class	DnaReferenceImpl
class	DnaRegionImpl
class	DnaRegionReferenceImpl
class	EntityFeatureImpl
class	EntityImpl
class	EntityReferenceImpl
class	EntityReferenceTypeVocabularyImpl
class	EvidenceCodeVocabularyImpl
class	EvidenceImpl
class	ExperimentalFormImpl
class	ExperimentalFormVocabularyImpl
class	FragmentFeatureImpl
class	GeneImpl
class	GeneticInteractionImpl
class	InteractionImpl
class	InteractionVocabularyImpl
class	KPrimeImpl
class	L3ElementImpl	Base BioPAX Level3 element.
class	ModificationFeatureImpl
class	ModulationImpl
class	MolecularInteractionImpl
class	NamedImpl
class	NucleicAcidImpl
class	NucleicAcidReferenceImpl
class	NucleicAcidRegionReferenceImpl
class	PathwayImpl
class	PathwayStepImpl
class	PhenotypeVocabularyImpl
class	PhysicalEntityImpl
class	ProcessImpl
class	ProteinImpl
class	ProteinReferenceImpl
class	ProvenanceImpl
class	PublicationXrefImpl
class	RelationshipTypeVocabularyImpl
class	RelationshipXrefImpl
class	RnaImpl
class	RnaReferenceImpl
class	RnaRegionImpl
class	RnaRegionReferenceImpl
class	ScoreImpl
class	SequenceEntityReferenceImpl
class	SequenceIntervalImpl
class	SequenceLocationImpl
class	SequenceModificationVocabularyImpl
class	SequenceRegionVocabularyImpl
class	SequenceSiteImpl
class	SimplePhysicalEntityImpl
class	SmallMoleculeImpl
class	SmallMoleculeReferenceImpl
class	StoichiometryImpl
class	TemplateReactionImpl
class	TemplateReactionRegulationImpl
class	TissueVocabularyImpl
class	TransportImpl
class	TransportWithBiochemicalReactionImpl
class	UnificationXrefImpl
class	XReferrableImpl	This class helps with managing the bidirectional xref links.
class	XrefImpl

Uses of Level3Element in org.biopax.paxtools.model.level3

Subinterfaces of Level3Element in org.biopax.paxtools.model.level3

Modifier and Type	Interface	Description
interface	BindingFeature
interface	BiochemicalPathwayStep	Definition: Imposes ordering on a step in a biochemical pathway.
interface	BiochemicalReaction	Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
interface	BioSource	Definition: The biological source of an entity (e.g.
interface	Catalysis	Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
interface	CellularLocationVocabulary	Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
interface	CellVocabulary	Definition: A reference to the Cell Type Ontology (CL).
interface	ChemicalConstant
interface	ChemicalStructure	Definition: The chemical structure of a small molecule.
interface	Complex	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.
interface	ComplexAssembly	Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
interface	Control	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
interface	ControlledVocabulary	Definition: This class represents a term from an external controlled vocabulary (CV).
interface	Controller	This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
interface	Conversion	Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.
interface	CovalentBindingFeature	Definition: An entity feature that represent the covalently bound state of a physical entity.
interface	Degradation	Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.
interface	DeltaG	Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
interface	Dna	Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
interface	DnaReference	A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
interface	DnaRegion	Definition: A region on a DNA molecule.
interface	DnaRegionReference	Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
interface	Entity	This class represents a discrete biological unit used when describing pathways.
interface	EntityFeature	Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
interface	EntityReference	Definition: An entity reference is a grouping of several physical entities across different contexts and molecular states, that share common physical properties and often named and treated as a single entity with multiple states by biologists.
interface	EntityReferenceTypeVocabulary	Definiiton: A reference to a term from an entity reference group ontology.
interface	Evidence	Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
interface	EvidenceCodeVocabulary	Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
interface	ExperimentalForm	Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
interface	ExperimentalFormVocabulary	Definition: A term that describes the form of the physical entity in the context of the experiment.
interface	FragmentFeature	Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
interface	Gene	Definition: A continuant that encodes information that can be inherited through replication.
interface	GeneticInteraction	Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
interface	Interaction	Definition: A biological relationship between two or more entities.
interface	InteractionVocabulary	A reference to the PSI Molecular Interaction ontology (MI) interaction type.
interface	KPrime	The apparent equilibrium constant, K', and associated values.
interface	ModificationFeature	Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.
interface	Modulation	Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
interface	MolecularInteraction	Definition: An interaction in which at least one participant is a physical entity, e.g.
interface	Named	Interface for all classes that can have names in BioPAX.
interface	NucleicAcid	Tagger interface for DNA and RNA
interface	NucleicAcidReference	Role interface for NucleicAcidReferences, namely DNA and RNA.
interface	NucleicAcidRegionReference
interface	Observable	User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
interface	Pathway
interface	PathwayStep	This represents a set of pathway events.
interface	PhenotypeVocabulary
interface	PhysicalEntity
interface	Process	Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
interface	Protein
interface	ProteinReference	Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.
interface	Provenance	Definition: The direct source of a pathway data or score.
interface	PublicationXref
interface	RelationshipTypeVocabulary	Vocabulary for defining relationship Xref types.
interface	RelationshipXref	Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
interface	Rna
interface	RnaReference
interface	RnaRegion	Definition: A region on a RNA molecule.
interface	RnaRegionReference	A RNA region reference
interface	Score	Definition: A score associated with a publication reference describing how the score was determined, the name of the method and a comment briefly describing the method.
interface	SequenceEntity	Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
interface	SequenceEntityReference	Tagger interface for protein, dna and rna entities
interface	SequenceInterval
interface	SequenceLocation	Definition: A location on a nucleotide or amino acid sequence.
interface	SequenceModificationVocabulary	Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.
interface	SequenceRegionVocabulary	Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.
interface	SequenceSite
interface	SimplePhysicalEntity	Tagger interface for non-complex physical entities
interface	SmallMolecule
interface	SmallMoleculeReference
interface	Stoichiometry	Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
interface	TemplateReaction
interface	TemplateReactionRegulation
interface	TissueVocabulary	Definition: A reference to the BRENDA
interface	Transport
interface	TransportWithBiochemicalReaction
interface	UnificationXref	Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity.
interface	UtilityClass
interface	Xref
interface	XReferrable