Molecular_Interaction_Maps/TranscriptionShorthand

TableOfContents([2])

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

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:

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

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)