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| Packages that use org.biopax.paxtools.model.level3 | |
|---|---|
| org.biopax.paxtools.controller | |
| org.biopax.paxtools.impl.level3 | |
| org.biopax.paxtools.model.level3 | |
| Classes in org.biopax.paxtools.model.level3 used by org.biopax.paxtools.controller | |
|---|---|
| EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological identity. |
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| 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. |
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| PhysicalEntity
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| Process
Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction |
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| Xref
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| XReferrable
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| Classes in org.biopax.paxtools.model.level3 used by org.biopax.paxtools.impl.level3 | |
|---|---|
| BindingFeature
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| BiochemicalPathwayStep
Definition: Imposes ordering on a step in a biochemical pathway. |
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| BiochemicalReaction
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). |
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| BioSource
Definition: The biological source of an entity (e.g. |
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| Catalysis
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. |
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| CatalysisDirectionType
This enum represents the direction of a catalysis under all physiological conditions if there is one. |
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| CellularLocationVocabulary
Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology. |
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| CellVocabulary
Definition: A reference to the Cell Type Ontology (CL). |
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| ChemicalStructure
Definition: The chemical structure of a small molecule. |
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| 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. |
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| ComplexAssembly
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g. |
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| Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e. |
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| ControlledVocabulary
Definition: This class represents a term from an external controlled vocabulary (CV). |
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| Controller
This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity. |
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| ControlType
Defines the nature of the control relationship between the controller and the controlled entities. |
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| 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. |
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| Degradation
Definition: A conversion in which a pool of macromolecules are degraded into their elementary units. |
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| DeltaG
Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o. |
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| Dna
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid. |
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| DnaReference
A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position. |
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| DnaRegion
Definition: A region on a DNA molecule. |
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| 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. |
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| 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". |
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| ExperimentalForm
Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design. |
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| ExperimentalFormVocabulary
Definition: A term that describes the form of the physical entity in the context of the experiment. |
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| FragmentFeature
Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event. |
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| Gene
Definition: A continuant that encodes information that can be inherited through replication. |
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| GeneticInteraction
Definition : Genetic interactions between genes occur when two genetic perturbations (e.g. |
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| Interaction
Definition: A biological relationship between two or more entities. |
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| InteractionVocabulary
A reference to the PSI Molecular Interaction ontology (MI) interaction type. |
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| KPrime
The apparent equilibrium constant, K', and associated values. |
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| Level3Element
A Level 3 specific element. |
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| ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification. |
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| Modulation
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another. |
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| MolecularInteraction
Definition: An interaction in which at least one participant is a physical entity, e.g. |
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| Named
Interface for all classes that can have names in BioPAX. |
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| NucleicAcid
Tagger interface for DNA and RNA |
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| NucleicAcidReference
Role interface for NucleicAcidReferences, namely DNA and RNA. |
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| NucleicAcidRegionReference
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| Observable
User: demir Date: Aug 17, 2007 Time: 5:47:27 PM |
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| Pathway
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| PathwayStep
This represents a set of pathway events. |
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| PhenotypeVocabulary
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| PhysicalEntity
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| PositionStatusType
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| Process
Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction |
|
| Protein
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| ProteinReference
Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence. |
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| Provenance
Definition: The direct source of a pathway data or score. |
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| PublicationXref
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| 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. |
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| Rna
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| RnaReference
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| RnaRegion
Definition: A region on a RNA molecule. |
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| RnaRegionReference
A RNA region reference |
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| 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. |
|
| SequenceEntityReference
Tagger interface for protein, dna and rna entities |
|
| SequenceInterval
|
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| 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. |
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| SequenceRegionVocabulary
Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org. |
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| SequenceSite
|
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| SimplePhysicalEntity
Tagger interface for non-complex physical entities |
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| SmallMolecule
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| SmallMoleculeReference
|
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| StepDirection
Catalysis direction controlled vocabulary |
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| Stoichiometry
Stoichiometric coefficient of a physical entity in the context of a conversion or complex. |
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| StructureFormatType
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| TemplateDirectionType
TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM |
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| TemplateReaction
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| TemplateReactionRegulation
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| TissueVocabulary
Definition: A reference to the BRENDA |
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| Transport
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| TransportWithBiochemicalReaction
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| 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 Rationale: Unification xrefs are critically important for data integration. |
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| UtilityClass
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| Xref
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| XReferrable
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|
| Classes in org.biopax.paxtools.model.level3 used by org.biopax.paxtools.model.level3 | |
|---|---|
| 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). |
|
| 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
|
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| 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. |
|
| 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
|
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| 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
|
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| TemplateDirectionType
TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM |
|
| TissueVocabulary
Definition: A reference to the BRENDA |
|
| Transport
|
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| UtilityClass
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| Xref
|
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| XReferrable
|
|
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