Use Case Name : ../ProcessStimulation

For Feature : MIMEditor

Editors: DavidKane

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A user wants specify that a species stimulates a reaction

Step-by-Step User Action

  1. User specifies a species to be the stimulator
  2. User specifies a reaction to be stimulated
  3. User specifies that there is a stimulation relationship
  4. User optionally specifies the evidence for the relationship

Visual Aides

The Kohn notation for process stimulation is the following:


An example using this notation follows:


Requirements for Cytoscape

Assuming that this can use the same approach that is used for ../ShowInhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: process stimulation), node2: A, node3: B

View: Use case for hyperedge view


This is of high 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 ../ShowNecessity. Other special casees include ../EnzymaticStimulation and ../EnzymaticStimulationInTrans, which have their own symbols.


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:


This example illustrates the concept of cooperative binding using the ../ProcessStimulation relationship.


Other Examples


Shared ../MimEditorUseCaseComments

This could be modeled in BioPAX as either a Control (for catalysts) or a Biochemical Reaction.

AllanKuchinsky - 2006-11-26 04:25:13 should be handled in the same way as for ShowInhibition

Molecular_Interaction_Maps/ProcessStimulation (last edited 2009-02-12 01:03:27 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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