## page was renamed from ProteinDomains
## These are wiki comments - leave them in so that people can see them when editing the page

## This template may be useful for documenting use cases 
## Developed in response to a hackathon request for formalized, detailed use cases 
##  to help direct implementation proposals

|| '''Use Case Name''' : ../ProteinDomains ||
|| '''For Feature''' : [[MIMEditor]]||
|| '''Editors''': DavidKane ||

## EXAMPLE: 
## Use Case Name: Representation of Protein Complex
## For Feature: Grouping Function
## Editors: Mr. Knowitall

<<TableOfContents([2])>>

== Summary ==
## Provide a one paragraph description of the use case
A user wants to describe interactions of a protein, domain by domain.

== Step-by-Step User Action ==
## Provide a step-by-step account of how the user would execute the use case.  For example: (1) right click on node, (2) choose "expand" from context menu, (3) new view is created, etc...

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

== Visual Aides ==
## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc)
An example of the notation for specifying protein domains follows:

{{attachment:proteindomains1_061117_dwk.PNG}}

== Requirements for Cytoscape ==
## List the components/functions already in Cytoscape that are relevant to the use case and possible implementations (e.g., "current context menus can be used accomplish step 2 above")
## Also list components/functions that are needed in Cytoscape to execute the use case (e.g., "cytoscape needs to allow for multiple views of the same network for this to work")
TBD

== Importance ==
## Describe whether this use case is critical and how frequently users would come across it.  Describe common work flows that might involve the use case (e.g., "this use case comes up regularly, on a weekly basis, whenever we want to analyze our protein superfamily networks").

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

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

{{attachment:proteindomains2_061117_dwk.PNG}}
 
The protein may be arranged vertically as well:
 
{{attachment:proteindomains3_061117_dwk.PNG}}

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.
 
{{attachment:proteindomains4_061117_dwk.PNG}}

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

{{attachment:proteindomains7_061117_dwk.PNG}}

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

{{attachment:proteindomains5_061117_dwk.PNG}}

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:

{{attachment:proteindomains6_061117_dwk.PNG}}

== Other Examples ==
## List other applications or relevant examples outside of Cytoscape that provide some or all of the desired functionality (e.g., "You can do this using the group function in PowerPoint").

== Comments ==

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