Use Case Name : ../TranscriptionShorthand

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe the possibility a protein is transcribed, without showing in detail, all of the mechanisms.

Step-by-Step User Action

  1. User specifies a protein to transcribe
  2. User optionally specifies another species that originates the transcription process
  3. User specifies that there is a ../TranscriptionShorthand relationship between the two

  4. User optionally specifies the evidence for this reaction

Visual Aides

The symbol for ../TranscriptionShorthand is simular to ../ProductAppears, except that there are a pair of right angles near the head:


An example in context follows:


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


Might be represented more simply as follows:


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. transcriptionshorthand4_061121_dwk.PNG

Requirements for Cytoscape



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

Other Examples


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)

Molecular_Interaction_Maps/TranscriptionShorthand (last edited 2009-02-12 01:04:15 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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