Diff for "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

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