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## page was renamed from Molecular Interaction Maps/Transport ## page was renamed from Transport |
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|| '''Use Case Name''' : Transport || || '''For Feature''' : Self:MIMEditor || |
|| '''Use Case Name''' : ../ShowTransport || || '''For Feature''' : [[MIMEditor]] || |
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| [[TableOfContents([2])]] | <<TableOfContents([2])>> |
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{{attachment:transport1_061115_dwk.png}} |
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== Variations == Membranes may be rendered with a thick double line. Some previous Kohn maps used a single line as well, but that convention does not need to be supported by the Self:MIMEditor. |
== Variations == Membranes are rendered with a thick double line. (See ../DefineCompartment) |
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{{attachment:transport2_061115_dwk.png}} |
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{{attachment:transport3_061115_dwk.png}} |
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| The transport use case is actually a special case of a stochimetric conversion, in which the source and the product are the same. | |
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| Shared MimEditorUseCaseComments |
Shared ../MimEditorUseCaseComments Some previous Kohn maps used a single line as well, but that convention does not need to be supported by the [[MIMEditor]]. |
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| 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. | 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. |
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---- AllanKuchinsky - 2007-01-19 03:07:58 see comments on DefineCompartment. At the model level, the concept of a Group in Cytoscape should support compartments. At the view level, we need to consider whether compartments are placed on the network canvas or should be on a background canvas. |
<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>
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:
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)
If the protein is involved in reactions after being transported across the membrane, then edges for those reactions, connect to the small black dot.
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.
AllanKuchinsky - 2007-01-19 03:07:58
see comments on DefineCompartment. At the model level, the concept of a Group in Cytoscape should support compartments. At the view level, we need to consider whether compartments are placed on the network canvas or should be on a background canvas.