Cytoscape Wiki|
← Revision 4 as of 2006-11-17 16:38:36
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← Revision 5 as of 2006-11-17 20:51:31 →
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| Deletions are marked like this. | Additions are marked like this. |
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| || '''Use Case Name''' : Transport || | || '''Use Case Name''' : ../ShowTransport || |
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| Membranes are rendered with a thick double line. (See Self:Compartment) | Membranes are rendered with a thick double line. (See ../DefineCompartment) |
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| Shared MimEditorUseCaseComments | Shared ../MimEditorUseCaseComments |
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| Transport is a special case of StoichiometricConversion – converting one molecule in one Self:Compartment to one molecule in another Self:Compartment without net change in the number of molecules overall. | Transport is a special case of ../StoichiometricConversion – converting one molecule in one compartment to one molecule in another compartment without net change in the number of molecules overall. |
Summary
A user wants to describe the possibility that protein is transported across a membrane from one compartment into another.
Step-by-Step User Action
- User specifies a species to be transported
- User specifies a starting compartment
- User specifies a destination compartment
- User optionally specifies the evidence for this relationship
Visual Aides
An example of Kohn notation for transportation:
attachment:transport1_061115_dwk.png
Requirements for Cytoscape
TBD
Importance
Being able to specify a compartment for a reaction, and to move species between compartments is critical for many maps.
Variations
Membranes are rendered with a thick double line. (See ../DefineCompartment)
attachment:transport2_061115_dwk.png
If the protein is involved in reactions after being transported across the membrane, then edges for those reactions, connect to the small black dot.
attachment:transport3_061115_dwk.png
Other Examples
Comments
Shared ../MimEditorUseCaseComments
Some previous Kohn maps used a single line as well, but that convention does not need to be supported by the MIMEditor.
The BioPAX representation of this binding could be a Transport object, but it is not clear how to specify the compartments the species is being transported from and to.
Transport is a special case of ../StoichiometricConversion – converting one molecule in one compartment to one molecule in another compartment without net change in the number of molecules overall.