PathwayStep#

class biopax-explorer.biopax.pathwaystep.PathwayStep(*args, **kwargs)[source]#

Bases: UtilityClass

Class PathwayStep

Definition: A step in an ordered pathway. Rationale: Some pathways can have a

temporal order. For example, if the pathway boundaries are based on a perturbation phenotype link, the pathway might start with the perturbing agent and end at gene expression leading to the observed changes. Pathway steps can represent directed compound graphs. Usage: Multiple interactions may occur in a pathway step, each should be listed in the stepProcess property. Order relationships between pathway steps may be established with the nextStep slot. If the reaction contained in the step is a reversible biochemical reaction but physiologically has a direction in the context of this pathway, use the subclass BiochemicalPathwayStep. Example: A metabolic pathway may contain a pathway step composed of one biochemical reaction (BR1) and one catalysis (CAT1) instance, where CAT1 describes the catalysis of BR1. The M phase of the cell cycle, defined as a pathway, precedes the G1 phase, also defined as a pathway.

code generator : rdfobj (author F.Moreews 2023-2024).

Methods

`get_comment`()	Attribute _comment getter
`get_evidence`()	Attribute _evidence getter
`get_nextStep`()	Attribute _nextStep getter
`get_stepProcess`()	Attribute _stepProcess getter

attribute_type_by_name
get_uri_string
object_attributes
set_comment
set_evidence
set_nextStep
set_stepProcess
set_uri_string
to_json
type_attributes

Methods Summary

`attribute_type_by_name`()
`get_evidence`()	Attribute _evidence getter
`get_nextStep`()	Attribute _nextStep getter
`get_stepProcess`()	Attribute _stepProcess getter
`get_uri_string`()
`object_attributes`()
`set_evidence`(value)
`set_nextStep`(value)
`set_stepProcess`(value)
`set_uri_string`(uristr)
`to_json`()
`type_attributes`()

Methods Documentation

attribute_type_by_name()[source]#

get_evidence()[source]#

Attribute _evidence getter: Scientific evidence supporting the existence of the entity as described.

get_nextStep()[source]#

Attribute _nextStep getter
The next step(s) of the pathway. Contains zero or more pathwayStep instances.

If there is no next step, this property is empty. Multiple pathwayStep instances indicate pathway branching.

get_stepProcess()[source]#

Attribute _stepProcess getter: An interaction or a pathway that are a part of this pathway step.

get_uri_string()[source]#

object_attributes()[source]#

set_evidence(value)[source]#

set_nextStep(value)[source]#

set_stepProcess(value)[source]#

set_uri_string(uristr)[source]#

to_json()[source]#

type_attributes()[source]#