See: Description
Interface | 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.
|
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 . |
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. |
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 | |
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 | |
Stoichiometry |
Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
|
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 Rationale: Unification xrefs are critically important for data
integration.
|
UtilityClass | |
Xref | |
XReferrable |
Enum | Description |
---|---|
CatalysisDirectionType |
This enum represents the direction of a catalysis under all physiological conditions if there is one.
|
ControlType |
Defines the nature of the control relationship between the controller and the controlled entities.
|
ConversionDirectionType |
This enum is used for specifying the direction of a Conversion.
|
PositionStatusType | |
StepDirection |
Catalysis direction controlled vocabulary
|
StructureFormatType | |
TemplateDirectionType |
TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
|
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