## page was renamed from Molecular Interaction Maps/Necessity ## page was renamed from Necessity ## 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''' : ../ShowNecessity || || '''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 species is necessary for the completion of another reaction. == 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 reaction that is being regulated 1. User specifies a species that is necessary for the reaction to complete 1. User specifies the necessity relationship 1. User optionally specifies the evidence for this reaction == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The Kohn notation for this reaction is the following: {{attachment:necessity1_061115_dwk.png}} Here is an example of how this symbol would be applied: {{attachment:necessity2_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") Could be modeled as a Hyperedge containing node1: C (hyperedge attribute: necessity), node2: A, node3: B View: Use case for hyperedge view == 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 one of several reaction modifiers. There are several other structurally similar relationships. It can also be viewed as a special case of stimulation. == Variations == Named molecular species are not the only elements that can be specified as necessary. Users can specify that a modfied molecule or a process is necessary for a reaction. For example the following example shows that phosphorylation of a molecule A is required for the catalysis of the stoichiometric conversion of B to C by A: {{attachment:necessity3a_061115_dwk.PNG}} This example shows the concept of Sequential Binding using the Necessity relationship: {{attachment:necessity4_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 Necessity could be represented in BioPAX either as a Control (for catalysts) or a Biochemical Reaction, but BioPax does not appear to have a direct concept of necessity. ---- AllanKuchinsky - 2006-11-21 15:42:47   view: looks as if it would require two new line types to represent activation and catalysis.   model: group implementation necessary to show domains and interactions to them. ---- AllanKuchinsky - 2007-01-19 03:16:22   Could this be represented using the Modifier node construct of hyperedges?