## page was renamed from Molecular Interaction Maps/Degradation ## page was renamed from Degradation ## 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''' : ../SpeciesDegradation || || '''For Feature''' : [[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 describe the possibility that a protein is degraded as part of a ../StoichiometricConversion. == 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 degraded 1. User specifies a ../StoichiometricConversion with this protein 1. User specifies the result of the conversion is degradation 1. User specifies the evidence for this relationship == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The Kohn notation for degradation is the following: {{attachment:degradation1_061115_dwk.png}} An example of the degradation symbol used as the result of a conversion follows: {{attachment:degradation2_061115_dwk.png}} The color in this example is convention, and is not an essential element in the notation. == 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"). This is a fairly common reaction. == 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 In the context of a ../StoichiometricConversion, the BioPax representation would basically be the same as any other ../StoichiometricConversion, except that the degradation products would be described as small molecules, which would not be used in subsequent reactions. ---- AllanKuchinsky - 2007-01-22 05:15:47   Is there the need for special 'constant' Node(s) in Cytoscape to represent constructs like degradation?  Are there special semantics associated with degradation 'nodes', e.g. would one ever want to assign attributes to a particular degradation 'node'?