|
Interface Summary |
| 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). |
| 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. |
| 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 |
|