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1. User 1. ... 1. ... |
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 |
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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}} |
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| TBD | This is a fairly common structure, and is of moderate importance. |
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---- 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 |
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| [[PageComment2]] | Does there need to be a Cytoscape 'constant' node for 'mRNA'? (see comments for SpeciesDegradation) |
Use Case Name : ../TranscriptionShorthand |
For Feature : MIMEditor |
Editors: DavidKane |
<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>
Summary
A user wants to describe the possibility a protein is transcribed, without showing in detail, all of the mechanisms.
Step-by-Step User Action
- User specifies a protein to transcribe
- User optionally specifies another species that originates the transcription process
User specifies that there is a ../TranscriptionShorthand relationship between the two
- 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. 
Requirements for Cytoscape
TBD
Importance
This is a fairly common structure, and is of moderate importance.
Other Examples
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)