Use Case Name : ../ShowNecessity

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe the possibility that a species is necessary for the completion of another reaction.

Step-by-Step User Action

  1. User specifies a reaction that is being regulated
  2. User specifies a species that is necessary for the reaction to complete
  3. User specifies the necessity relationship
  4. 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


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.


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


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?

Molecular_Interaction_Maps/ShowNecessity (last edited 2009-02-12 01:03:02 by localhost)

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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