Cytoscape Wiki
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 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 MIMEditor.
If the protein is involved in reactions after being transported across the membrane, then edges for those reactions, connect to the small black dot.
The transport use case is actually a special case of a stochimetric conversion, in which the source and the product are the same.
Other Examples
Comments
Shared MimEditorUseCaseComments
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.