Use Case Name : ../ShowTransport

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe the possibility that protein is transported across a membrane from one compartment into another.

Step-by-Step User Action

  1. User specifies a species to be transported
  2. User specifies a starting compartment
  3. User specifies a destination compartment
  4. User optionally specifies the evidence for this relationship

Visual Aides

An example of Kohn notation for transportation:


Requirements for Cytoscape



Being able to specify a compartment for a reaction, and to move species between compartments is critical for many maps.


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


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.  

Molecular_Interaction_Maps/ShowTransport (last edited 2009-02-12 01:03:33 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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