## page was renamed from SaveBioPax ## 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''' : ../SaveBioPax || || '''For Feature''' : self:MIMEditor || || '''Editors''': DavidKane || ## EXAMPLE: ## Use Case Name: Representation of Protein Complex ## For Feature: Grouping Function ## Editors: Mr. Knowitall <> == Summary == ## Provide a one paragraph description of the use case A user wants to save a BioPax representation of a map. == 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 has edited a map 1. The user specifies that the map is to be saved 1. The systems writes out an appropriate BioPax repressentation == 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") 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"). Many pathway repositories are moving towards adopting BioPax as a standard of exchange. If the Kohn maps are exchangeable as BioPax, they could be exchanged and used more widely. == 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 It is not clear if saving as BioPax should be part of how the maps are normally saved, or if BioPax should be a “Save As” option. It is also not clear how to pair the visualization layout information with the BioPax representation. ---- AllanKuchinsky - 2007-01-23 05:18:23   This would be subsumed by general BioPAX export functionality in Cytoscape.  What are current plans for this? Would XGMML be a good vehicle for storing the visual layout information?  If that is the case, then would we want to build on top of the 'session' abstraction to store/retrieve associated BioPAX and XGMML representations of networks?