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Summary
A user wants to describe the possibility that a species is necessary for the completion of another reaction.
Step-by-Step User Action
- User specifies a reaction that is being regulated
- User specifies a species that is necessary for the reaction to complete
- User specifies the necessity relationship
- User optionally specifies the evidence for this reaction
Visual Aides
The Kohn notation for this reaction is the following:
Here is an example of how this symbol would be applied:
The color in this example is convention, and is not an essential element in the notation.
Requirements for Cytoscape
Could be modeled as a Hyperedge containing node1: C (hyperedge attribute: necessity), node2: A, node3: B View: Use case for hyperedge view
Importance
This is one of several reaction modifiers. There are several other structurally similar relationships. It can also be viewed as a special case of stimulation.
Variations
Named molecular species are not the only elements that can be specified as necessary. Users can specify that a modfied molecule or a process is necessary for a reaction. For example the following example shows that phosphorylation of a molecule A is required for the catalysis of the stoichiometric conversion of B to C by A:
This example shows the concept of Sequential Binding using the Necessity relationship:
Other Examples
Comments
Shared ../MimEditorUseCaseComments
Necessity could be represented in BioPAX either as a Control (for catalysts) or a Biochemical Reaction, but BioPax does not appear to have a direct concept of necessity.
AllanKuchinsky - 2006-11-21 15:42:47
view: looks as if it would require two new line types to represent activation and catalysis.
model: group implementation necessary to show domains and interactions to them.
AllanKuchinsky - 2007-01-19 03:16:22
Could this be represented using the Modifier node construct of hyperedges?