Molecular_Interaction_Maps/ProcessStimulation

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

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 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