Package org.biopax.paxtools.model.level3
package org.biopax.paxtools.model.level3
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
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ClassDescriptionDefinition: Imposes ordering on a step in a biochemical pathway.Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).Definition: The biological source of an entity (e.g.Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.This enum represents the direction of a catalysis under all physiological conditions if there is one.Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.Definition: A reference to the Cell Type Ontology (CL).Definition: The chemical structure of a small molecule.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.Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.Definition: This class represents a term from an external controlled vocabulary (CV).This is a role interface for pathway elements that can control processes, namely
PathwayandPhysicalEntity.Defines the nature of the control relationship between the controller and the controlled entities.Definition: An interaction in which molecules of one or morePhysicalEntitypools are physically transformed and become a member of one or more other PhysicalEntity pools.This enum is used for specifying the direction of a Conversion.Definition: An entity feature that represent the covalently bound state of a physical entity.Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.Definition: A region on a DNA molecule.Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.This class represents a discrete biological unit used when describing pathways.Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.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.Definiiton: A reference to a term from an entity reference group ontology.Definition: The support for a particular assertion, such as the existence of an interaction or pathway.Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.Definition: A term that describes the form of the physical entity in the context of the experiment.Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.Definition: A continuant that encodes information that can be inherited through replication.Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.Definition: A biological relationship between two or more entities.A reference to the PSI Molecular Interaction ontology (MI) interaction type.The apparent equilibrium constant, K', and associated values.A Level 3 specific element.Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.Definition: An interaction in which at least one participant is a physical entity, e.g.Interface for all classes that can have names in BioPAX.Tagger interface for DNA and RNARole interface for NucleicAcidReferences, namely DNA and RNA.User: demir Date: Aug 17, 2007 Time: 5:47:27 PMThis represents a set of pathway events.Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and InteractionDescription: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.Definition: The direct source of a pathway data or score.Vocabulary for defining relationship Xref types.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.Definition: A region on a RNA molecule.A RNA region referenceDefinition: 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.Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.Tagger interface for protein, dna and rna entitiesDefinition: A location on a nucleotide or amino acid sequence.Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.Tagger interface for non-complex physical entitiesCatalysis direction controlled vocabularyStoichiometric coefficient of a physical entity in the context of a conversion or complex.TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AMDefinition: A reference to the BRENDADefinition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity.