Uses of Package
org.biopax.paxtools.model.level3

Packages that use org.biopax.paxtools.model.level3

Package	Description
org.biopax.paxtools.controller	This package contains various methods and algorithms for traversing and manipulating the model.
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.

Classes in org.biopax.paxtools.model.level3 used by org.biopax.paxtools.controller

Class	Description
BioSource	Definition: The biological source of an entity (e.g.
Control	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
EntityFeature	Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
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.
Pathway
PhysicalEntity
Provenance	Definition: The direct source of a pathway data or score.
SimplePhysicalEntity	Tagger interface for non-complex physical entities

Classes in org.biopax.paxtools.model.level3 used by org.biopax.paxtools.impl.level3

Class	Description
BindingFeature
BiochemicalPathwayStep	Definition: Imposes ordering on a step in a biochemical pathway.
BiochemicalReaction	Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
BioSource	Definition: The biological source of an entity (e.g.
Catalysis	Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
CatalysisDirectionType	This enum represents the direction of a catalysis under all physiological conditions if there is one.
CellularLocationVocabulary	Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
CellVocabulary	Definition: A reference to the Cell Type Ontology (CL).
ChemicalConstant
ChemicalStructure	Definition: The chemical structure of a small molecule.
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.
ComplexAssembly	Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
Control	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
ControlledVocabulary	Definition: This class represents a term from an external controlled vocabulary (CV).
Controller	This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
ControlType	Defines the nature of the control relationship between the controller and the controlled entities.
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.
ConversionDirectionType	This enum is used for specifying the direction of a Conversion.
CovalentBindingFeature	Definition: An entity feature that represent the covalently bound state of a physical entity.
Degradation	Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.
DeltaG	Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
Dna	Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
DnaReference	A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
DnaRegion	Definition: A region on a DNA molecule.
DnaRegionReference	Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
Entity	This class represents a discrete biological unit used when describing pathways.
EntityFeature	Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
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.
EntityReferenceTypeVocabulary	Definiiton: A reference to a term from an entity reference group ontology.
Evidence	Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
EvidenceCodeVocabulary	Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
ExperimentalForm	Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
ExperimentalFormVocabulary	Definition: A term that describes the form of the physical entity in the context of the experiment.
FragmentFeature	Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
Gene	Definition: A continuant that encodes information that can be inherited through replication.
GeneticInteraction	Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
Interaction	Definition: A biological relationship between two or more entities.
InteractionVocabulary	A reference to the PSI Molecular Interaction ontology (MI) interaction type.
KPrime	The apparent equilibrium constant, K', and associated values.
Level3Element	A Level 3 specific element.
ModificationFeature	Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.
Modulation	Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
MolecularInteraction	Definition: An interaction in which at least one participant is a physical entity, e.g.
Named	Interface for all classes that can have names in BioPAX.
NucleicAcid	Tagger interface for DNA and RNA
NucleicAcidReference	Role interface for NucleicAcidReferences, namely DNA and RNA.
NucleicAcidRegionReference
Observable	User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
Pathway
PathwayStep	This represents a set of pathway events.
PhenotypeVocabulary
PhysicalEntity
PositionStatusType
Process	Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
Protein
ProteinReference	Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.
Provenance	Definition: The direct source of a pathway data or score.
PublicationXref
RelationshipTypeVocabulary	Vocabulary for defining relationship Xref types.
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.
Rna
RnaReference
RnaRegion	Definition: A region on a RNA molecule.
RnaRegionReference	A RNA region reference
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.
SequenceEntity	Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
SequenceEntityReference	Tagger interface for protein, dna and rna entities
SequenceInterval
SequenceLocation	Definition: A location on a nucleotide or amino acid sequence.
SequenceModificationVocabulary	Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.
SequenceRegionVocabulary	Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.
SequenceSite
SimplePhysicalEntity	Tagger interface for non-complex physical entities
SmallMolecule
SmallMoleculeReference
StepDirection	Catalysis direction controlled vocabulary
Stoichiometry	Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
StructureFormatType
TemplateDirectionType	TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
TemplateReaction
TemplateReactionRegulation
TissueVocabulary	Definition: A reference to the BRENDA
Transport
TransportWithBiochemicalReaction
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.
UtilityClass
Xref
XReferrable

Classes in org.biopax.paxtools.model.level3 used by org.biopax.paxtools.model.level3

Class	Description
BindingFeature
BiochemicalReaction	Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
BioSource	Definition: The biological source of an entity (e.g.
CatalysisDirectionType	This enum represents the direction of a catalysis under all physiological conditions if there is one.
CellularLocationVocabulary	Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
CellVocabulary	Definition: A reference to the Cell Type Ontology (CL).
ChemicalConstant
ChemicalStructure	Definition: The chemical structure of a small molecule.
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.
Control	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
ControlledVocabulary	Definition: This class represents a term from an external controlled vocabulary (CV).
Controller	This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
ControlType	Defines the nature of the control relationship between the controller and the controlled entities.
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.
ConversionDirectionType	This enum is used for specifying the direction of a Conversion.
DeltaG	Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
Entity	This class represents a discrete biological unit used when describing pathways.
EntityFeature	Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
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.
EntityReferenceTypeVocabulary	Definiiton: A reference to a term from an entity reference group ontology.
Evidence	Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
EvidenceCodeVocabulary	Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
ExperimentalForm	Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
ExperimentalFormVocabulary	Definition: A term that describes the form of the physical entity in the context of the experiment.
Interaction	Definition: A biological relationship between two or more entities.
InteractionVocabulary	A reference to the PSI Molecular Interaction ontology (MI) interaction type.
KPrime	The apparent equilibrium constant, K', and associated values.
Level3Element	A Level 3 specific element.
ModificationFeature	Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.
Named	Interface for all classes that can have names in BioPAX.
NucleicAcid	Tagger interface for DNA and RNA
NucleicAcidReference	Role interface for NucleicAcidReferences, namely DNA and RNA.
NucleicAcidRegionReference
Observable	User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
Pathway
PathwayStep	This represents a set of pathway events.
PhenotypeVocabulary
PhysicalEntity
PositionStatusType
Process	Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
Provenance	Definition: The direct source of a pathway data or score.
RelationshipTypeVocabulary	Vocabulary for defining relationship Xref types.
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.
SequenceEntity	Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
SequenceEntityReference	Tagger interface for protein, dna and rna entities
SequenceLocation	Definition: A location on a nucleotide or amino acid sequence.
SequenceModificationVocabulary	Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.
SequenceRegionVocabulary	Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.
SequenceSite
SimplePhysicalEntity	Tagger interface for non-complex physical entities
StepDirection	Catalysis direction controlled vocabulary
Stoichiometry	Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
StructureFormatType
TemplateDirectionType	TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
TissueVocabulary	Definition: A reference to the BRENDA
Transport
UtilityClass
Xref
XReferrable