Use Case Name : ProcessStimulation

For Feature : MIMEditor

Editors: DavidKane

TableOfContents([2])

Summary

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:

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

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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