Use Case Name : ../DefineProcess

For Feature : MIMEditor

Editors: DavidKane

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A user wants to add a high-level process to a map.

Step-by-Step User Action

  1. User specifies that a process should be added
  2. User labels the process
  3. User optionally associates the process with other maps

Visual Aides

A process is represented with a labeled box:


Process can serve as inputs as well as outputs in maps. For example exposure to a drug can be a process that originates an interaction (e.g. inhibition).

Requirements for Cytoscape



Many maps refer to processes that are important in the context of the map, even if the details of the process are not. A process is an abstraction of those activities.

Other Examples


Shared ../MimEditorUseCaseComments

A process differs from a ../VirtualCompartment, in that species can go into a ../VirtualCompartment by way of binding. A process has no notion of inside or outside.

AllanKuchinsky - 2006-12-11 03:29:43

At the model level, should this be represented as a group? Probably not if it is not expandable. Should this just be represented as a CyNode of a certain type that has different visual characteristics? If so, then what are the implications for graph theoretic analysis, e.g. shortest path?

At the other extreme, could this be represented as an arbitrary graphical annotation? Would it have attributes?

Would a Process ever serve as a link to a separate map, i.e. perform some UI gesture such as double-clicking on the Process node and have a new map come up in a separate view?

MiritAladjem - 2006-12-13 12:30:39

Allan, thanks for the comments. It will be most useful to allo a process to be linked to another map. However, in the map where the process is represented as above, it will not be expandable.

Molecular_Interaction_Maps/DefineProcess (last edited 2009-02-12 01:03:27 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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