## page was renamed from Molecular Interaction Maps/Inhibition
## page was renamed from Inhibition
## These are wiki comments - leave them in so that people can see them when editing the page

## This template may be useful for documenting use cases 
## Developed in response to a hackathon request for formalized, detailed use cases 
##  to help direct implementation proposals

|| '''Use Case Name''' : ../ShowInhibition ||
|| '''For Feature''' : MIM Editor ||
|| '''Editors''': DavidKane||

## EXAMPLE: 
## Use Case Name: Representation of Protein Complex
## For Feature: Grouping Function
## Editors: Mr. Knowitall

<<TableOfContents([2])>>

== Summary ==
## Provide a one paragraph description of the use case
A user wants to describe the possibility that one species can inhibit the completion of another reaction.

== Step-by-Step User Action ==
## Provide a step-by-step account of how the user would execute the use case.  For example: (1) right click on node, (2) choose "expand" from context menu, (3) new view is created, etc...

 1. User specifies a species; this is the inhibiting agent
 1. User specifies the reaction that is to be inhibited
 1. User specifies the inhibition relationship
 1. User optionally specifies the evidence for this reaction

== Visual Aides ==
## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc)
The Kohn notation for this reaction is the following:

{{attachment:inhibition1_061115_dwk.png}}

Here is an example of how this symbol would be applied:

{{attachment:inhibition2_061115_dwk.png}}

The color in this example is convention, and is not an essential element in the notation.

== Requirements for Cytoscape ==
## List the components/functions already in Cytoscape that are relevant to the use case and possible implementations (e.g., "current context menus can be used accomplish step 2 above")
## Also list components/functions that are needed in Cytoscape to execute the use case (e.g., "cytoscape needs to allow for multiple views of the same network for this to work")
Could be modeled as a Hyperedge containing node1: C (hyperedge attribute: inhibition), node2: A, node3: B 

View: Use case for hyperedge view 

== Importance ==
## Describe whether this use case is critical and how frequently users would come across it.  Describe common work flows that might involve the use case (e.g., "this use case comes up regularly, on a weekly basis, whenever we want to analyze our protein superfamily networks").
This is one of several reaction modifiers, and it is very common in the maps.  There are several other structurally similar relationships.

== Other Examples ==
## List other applications or relevant examples outside of Cytoscape that provide some or all of the desired functionality (e.g., "You can do this using the group function in PowerPoint").

== Variations ==

This examples show the concept of Mutually Exclusive Binding using the inhibition relationship.

{{attachment:inhibition3_061117_dwk.png}}

== Comments ==
Shared ../MimEditorUseCaseComments 

 * The BioPAX representation could be either either a Control (for catalysts) or a Biochemical Reaction.

 *AllanKuchinsky
 *2006-11-17 03:40:50
  *Basic mechanism will be implemented in HyperEdge editor plugin for Cytoscape 2.4.