Interaction#
- class biopax-explorer.biopax.interaction.Interaction(*args, **kwargs)[source]#
Bases:
EntityClass Interaction
Definition: A biological relationship between two or more entities. Rationale:
In BioPAX, interactions are atomic from a database modeling perspective, i.e. interactions can not be decomposed into sub-interactions. When representing non- atomic continuants with explicit subevents the pathway class should be used instead. Interactions are not necessarily temporally atomic, for example genetic interactions cover a large span of time. Interactions as a formal concept is a continuant, it retains its identitiy regardless of time, or any differences in specific states or properties. Usage: Interaction is a highly abstract class and in almost all cases it is more appropriate to use one of the subclasses of interaction. It is partially possible to define generic reactions by using generic participants. A more comprehensive method is planned for BioPAX L4 for covering all generic cases like oxidization of a generic alcohol. Synonyms: Process, relationship, event. Examples: protein-protein interaction, biochemical reaction, enzyme catalysis
code generator : rdfobj (author F.Moreews 2023-2024).
Methods
get_availability()Attribute _availability getter
get_comment()Attribute _comment getter
get_dataSource()Attribute _dataSource getter
get_displayName()Attribute _displayName getter
get_evidence()Attribute _evidence getter
Attribute _interactionType getter
get_name()Attribute _name getter
Attribute _participant getter
get_standardName()Attribute _standardName getter
get_xref()Attribute _xref getter
attribute_type_by_name
get_uri_string
object_attributes
set_availability
set_comment
set_dataSource
set_displayName
set_evidence
set_interactionType
set_name
set_participant
set_standardName
set_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _interactionType getter
Attribute _participant getter
set_interactionType(value)set_participant(value)set_uri_string(uristr)to_json()Methods Documentation
- get_interactionType()[source]#
- Attribute _interactionType getter
Controlled vocabulary annotating the interaction type for example,
“phosphorylation reaction”. This annotation is meant to be human readable and may not be suitable for computing tasks, like reasoning, that require formal vocabulary systems. For instance, this information would be useful for display on a web page or for querying a database. The PSI-MI interaction type controlled vocabulary should be used. This is browsable at: http://www.ebi.ac.uk/ontology- lookup/browse.do?ontName=MI&termId=MI%3A0190&termName=interaction%20type
- get_participant()[source]#
- Attribute _participant getter
This property lists the entities that participate in this interaction. For
example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction. This property has a number of sub- properties, such as LEFT and RIGHT used in the biochemicalInteraction class. Any participant listed in a sub-property will automatically be assumed to also be in PARTICIPANTS by a number of software systems, including Protege, so this property should not contain any instances if there are instances contained in a sub-property.