Use Case Name : ../ProteinDomains

For Feature : MIMEditor

Editors: DavidKane

<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>


A user wants to describe interactions of a protein, domain by domain.

Step-by-Step User Action

  1. User specifies a protein to be described in more detail
  2. User specifies the number of domains to be included
  3. User specifies the name of each domain
  4. User then uses each domain in subsequent reactions

Visual Aides

An example of the notation for specifying protein domains follows:


Requirements for Cytoscape



For some maps, the key proteins have several protein domains of interest, and modeling with that level of detail is important for the map.


The domain can interact as any other species. E.g. in this case, Dom3 of protein A binds to protein B.


The protein may be arranged vertically as well:


It is also possible to model a trans-membrane protein, in which some portions of the protein exist in one Compartment, and some in another.


Earlier maps have the same concept with a slightly different graphical style, as in this example:


Protein domains can interact with each other, for example, by binding:


If a protein is described with domain detail, but it is unknown which domain an interaction is involved with, then the interaction is linked to the name of the protein instead:


Other Examples


Shared ../MimEditorUseCaseComments

AllanKuchinsky 2006-11-26 04:43:55

This requires the following support from Cytoscape: 1. ability to connect edges to members of groups as well as to the group itself (Cytoscape 2.5) 2. view groups as vertical or horizontal stacks (Cytoscape 2.5) 3. ability to mix nodes, edges, and arbitrary graphic annotations in groups (needed to support GenMAPP as well) 4. specialized rendering for certain kinds of groups, such as transmembrane proteins (would this be part of Cytoscape or part of specialized editing?).

AllanKuchinsky 2006-11-26 04:47:40

Do we need to have a representation for the 'blank' part of the protein/domain representation, i.e. the blank area at right of horizontal arrangement and bottom of vertical arrangement? Is this strictly part of the view or is it part of the model, as well? For example can you connect to the blank area?

AllanKuchinsky 2006-11-26 04:58:29

Addendum to point 4 in my first comment:

It appears that a specialized rendering is needed for all the domain representations specified on this page, although there is a good deal of commonality with some of the Group views that are planned for Cytoscape 2.5. The main distinction for showing domains in the manner above is that the bounding box does not include the protein itself, but the protein can still be connected. In a sense the bounding box in the view may need to be distinct from the 'bounding box' in the model. The editor will need to distinguish between a selection made within the visible bounding box and the a selection made within the model's 'bounding box'.

AllanKuchinsky 2006-11-26 05:01:06

This all requires a good deal more discussion with the people responsible for GroupAPI in Cytoscape

Molecular_Interaction_Maps/ProteinDomains (last edited 2009-02-12 01:03:02 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.

MoinMoin Appliance - Powered by TurnKey Linux