## 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''' : Black box pathways ||
|| '''For Feature''' : Groups ||
|| '''Editors''': Gary Bader ||

## 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
Sometimes it is useful to represent an entire pathway as a simple node or 'black box'. This is done either to simplify the pathway diagram, indicate connections to other pathways that are not the focus of the current map or represent generic or relatiively unknown processes. BioPAX allows a pathway to be defined using only a name, not any subcomponents.

== 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 can create a black box pathway, by creating a new node of type 'black box pathway'. This would be a group and user may add other nodes to it. A black box pathway node can be connected to any other node, including a group node.
 1. Or user can load an existing black box pathway from a BioPAX file

== Visual Aides ==
## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc)

== 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")
 * Similar to the requirements for other group use cases.  Some special requirements may exists for editing pathways that contain black box pathways, like having a special type of group node and being able to add nodes to the black box pathway.

== 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").
 * The PANTHER, PATIKA and INOH databases all allow black box pathways.  BioPAX supports this construct, however, it is not used that much.  It will become increasingly important as more signaling pathways are represented in BioPAX.

== 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 ==