Pathway#
- class biopax-explorer.biopax.pathway.Pathway(*args, **kwargs)[source]#
Bases:
EntityClass Pathway
Definition: A set or series of interactions, often forming a network, which
biologists have found useful to group together for organizational, historic, biophysical or other reasons. Usage: Pathways can be used for demarcating any subnetwork of a BioPAX model. It is also possible to define a pathway without specifying the interactions within the pathway. In this case, the pathway instance could consist simply of a name and could be treated as a ‘black box’. Pathways can also soverlap, i.e. a single interaction might belong to multiple pathways. Pathways can also contain sub-pathways. Pathways are continuants. Synonyms: network, module, cascade, Examples: glycolysis, valine biosynthesis, EGFR signaling
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
get_name()Attribute _name getter
Attribute _organism getter
Attribute _pathwayComponent getter
Attribute _pathwayOrder 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_name
set_organism
set_pathwayComponent
set_pathwayOrder
set_standardName
set_uri_string
set_xref
to_json
type_attributes
Methods Summary
Attribute _organism getter
Attribute _pathwayComponent getter
Attribute _pathwayOrder getter
set_organism(value)set_pathwayComponent(value)set_pathwayOrder(value)set_uri_string(uristr)to_json()Methods Documentation
- get_organism()[source]#
- Attribute _organism getter
An organism, e.g. ‘Homo sapiens’. This is the organism that the entity is found
in. Pathways may not have an organism associated with them, for instance, reference pathways from KEGG. Sequence-based entities (DNA, protein, RNA) may contain an xref to a sequence database that contains organism information, in which case the information should be consistent with the value for ORGANISM.
- get_pathwayComponent()[source]#
- Attribute _pathwayComponent getter
The set of interactions and/or pathwaySteps in this pathway/network. Each
instance of the pathwayStep class defines: 1) a set of interactions that together define a particular step in the pathway, for example a catalysis instance and the conversion that it catalyzes; 2) an order relationship to one or more other pathway steps (via the NEXT-STEP property). Note: This ordering is not necessarily temporal - the order described may simply represent connectivity between adjacent steps. Temporal ordering information should only be inferred from the direction of each interaction.
- get_pathwayOrder()[source]#
- Attribute _pathwayOrder getter
The ordering of components (interactions and pathways) in the context of this
pathway. This is useful to specific circular or branched pathways or orderings when component biochemical reactions are normally reversible, but are directed in the context of this pathway.