## 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''' : ../TranscriptionShorthand ||
|| '''For Feature''' : MIMEditor ||
|| '''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 a protein is transcribed, without showing in detail, all of the mechanisms. 

== 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 protein to transcribe
 1. User optionally specifies another species that originates the transcription process
 1. User specifies that there is a ../TranscriptionShorthand relationship between the two
 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 symbol for ../TranscriptionShorthand is simular to ../ProductAppears, except that there are a pair of right angles near the head:

{{attachment:transcriptionshorthand1_061120_dwk.PNG}}

An example in context follows:

{{attachment:transcriptionshorthand3_061121_dwk.PNG}}

The ../TranscriptionShorthand hides many of the transcription details.  So the following detailed representation show here:

{{attachment:transcriptionshorthand2_061120_dwk.PNG}}

Might be represented more simply as follows:

{{attachment:transcriptionshorthand2_061121_dwk.PNG}}

The ../TranscriptionShorthand concept differs from ../ProductAppears, in that in ../TranscriptionShorthand, the product must appear through transcription.  In ../ProductAppears, the product may appear through any mechanism. 
{{attachment:transcriptionshorthand4_061121_dwk.PNG}}

== 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")

TBD

== 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 a fairly common structure, and is of moderate importance.

== 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").

== Comments ==

Shared ../MimEditorUseCaseComments 

BioPax representation TBD 
----
GaryBader - 2006-12-26 12:26:48
 
This will be handled in BioPAX with the gene regulation proposal, currently under development for Level 3.
----
AllanKuchinsky - 2007-01-22 05:21:14
 
see my comments under TranscriptionInhibitionShorthand

Does there need to be a Cytoscape 'constant' node for 'mRNA'?  (see comments for SpeciesDegradation)