Use Case Name : ProcessStimulation |
For Feature : MIMEditor |
Editors: DavidKane |
Summary
A user wants specify that a species stimulates a reaction
Step-by-Step User Action
- User specifies a species to be the 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 process stimulation is the following:
attachment:processstimulation1_061115_dwk.png
An example using this notation follows:
attachment:processstimulation2_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: process stimulation), node2: A, node3: B
View: Use case for hyperedge view
Importance
Stimulation of biological process by molecules that do not directly participate in the process is very common in biology. In some cases a process is contingent upon another reaction – in this case the relationship is defined as a Necessity. Other special casees include EnzymaticStimulation and EnzymaticStimulationInTrans, which have their own symbols.
Variations
The stimulator does not necessarily have to be a molecular species; it can be a modified species or a process. In the example below, the phosphorylation of a molecule A enhances its ability to bind another molecule B:
attachment:processstimulation3_061115_dwk.png
Other Examples
Comments
Shared MimEditorUseCaseComments
This could be modeled in BioPAX as either a Control (for catalysts) or a Biochemical Reaction. PageComment2