Use Case Name : ../DefineCompartment

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe a membrane-enclosed compartment

Step-by-Step User Action

  1. User specifies a boundary to partition the compartments
  2. User optionally specifies a label for the compartments

Visual Aides

A membrane boundary is represented with a thick, double-walled line. It can either partition the entire map, as in this example:


Alternately, the compartment can completely enclose a region on a map, as in this example:


Requirements for Cytoscape


We are unsure to what degree components in the map need to be aware of what compartments they appear in.


Compartments play an important role in describing transportation functions. They also interact with other elements in the ../ShowTransport and ../ProteinDomains use cases.


Some earlier maps used a pattern instead of shading to describe the membrane as in this example:


Other Examples


Shared ../MimEditorUseCaseComments

It is not clear how to represent the compartments in BioPax.

AllanKuchinsky - 2006-11-26 05:41:17

Do compartments need to be aware of what components are in them? For example, if a compartment is moved or resized, do positions of components need to move with them or shift arrangement to accommodate resizing?

This requires further discussion, as there are a number of alternative ways that compartments could be represented: 1. as Groups, in which case components would be members. This raises the issue of whether Groups can intersect, e.g. for trans-membrane proteins. Since Groups are networks, this ought to be feasible, since nodes and edges can be shared across groups. But how would it affect intersecting groups if, for example, a compartment is moved or resized? 2. as arbitrary graphical annotations. Flexible, but doesn't accommodate the association of components with the compartment. 3. as a specialized type of Cytoscape Node. This seems as if it would require extensive changes and specialized processing in the Cytoscape core, probably not advisable.

MiritAladjem - 2007-02-01 08:53:38

Yes. Subcompartments and anything in the compartment needs to move when compartments are moved or resized.

Molecular_Interaction_Maps/DefineCompartment (last edited 2009-02-12 01:03:46 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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