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| Assuming that this can use the same approach that is used for self:Inhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation), node2: A, node3: B | Assuming that this can use the same approach that is used for Self:Inhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation), node2: A, node3: B |
Use Case Name : EnzymaticStimulation |
For Feature : MIMEditor |
Editors: DavidKane |
Summary
A user wants specify that a species is an enzyme that stimulates a reaction
Step-by-Step User Action
- User specifies a species to be the enzymatic stimulator
- User specifies a reaction to be stimulated
- User specifies that there is a stimulation relationship
- User optionally specifies the evidence for the relationship
Visual Aides
The Kohn notation for enzymatic stimulation is the following:
attachment:enzymaticstimulation1_061115_dwk.png
An example using this notation follows:
attachment:enzymaticstimulation2_061115_dwk.png
Requirements for Cytoscape
Assuming that this can use the same approach that is used for Inhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation), node2: A, node3: B
View: Use case for hyperedge view
Importance
TBD
Other Examples
Comments
Shared MimEditorUseCaseComments
This is a special case of a ProcessStimulation. The enzyme binds to the complex as part of the reaction, and is unmodified after the reaction.
This could be modeled in BioPAX as a Catalysis object (e.g. Catalysis object with participants = a physicalInteraction object and a enzyme A, Controlled = the physicalInteraction object, Controller=A, Control-Type = Activation, and Direction = IRREVERSIBLE-LEFT-TO-RIGHT)