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← Revision 1 as of 2006-11-15 21:10:07 →
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| || '''Use Case Name''' : ProcessStimulation || | || '''Use Case Name''' : ../ProcessStimulation || |
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| 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 | 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 |
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| 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. | 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. |
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attachment:processstimulation3_061115_dwk.png This example illustrates the concept of cooperative binding using the ../ProcessStimulation relationship. attachment:processstimulation4_061117_dwk.png |
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| Shared MimEditorUseCaseComments | Shared ../MimEditorUseCaseComments |
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 ../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
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 ../ShowNecessity. 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
This example illustrates the concept of cooperative binding using the ../ProcessStimulation relationship.
attachment:processstimulation4_061117_dwk.png
Other Examples
Comments
Shared ../MimEditorUseCaseComments
This could be modeled in BioPAX as either a Control (for catalysts) or a Biochemical Reaction. PageComment2