## page was renamed from Molecular Interaction Maps/Cleavage ## page was renamed from Cleavage ## 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''' : ../ShowCleavage || || '''For Feature''' : MIM Editor || || '''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 covalent bond can be cleaved. == 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 covalent bond that is to be cleaved 1. User specifies a species that acts to cleave the bond 1. User specifies that there is a cleaving relationship between the two 1. User optionally 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 this binding is the following. The species that is cleaving the bond is on end of the edge. The other end of the edge goes across the bond that is being cleaved. {{attachment:cleavage1_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") This could be modeled as a hyperedge containing node1: Phtase (hyperedge attribute: enzyme), node2: phosphorylated A, node3: unphosphorylated A. The mapping might be different if it is a protein that is being cleaved. View: Use case for hyperedge view. Might require a new line type in Vizmapper. == 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 important because it is a fairly common activity in the maps. In addition, it is an example of a reversal of another reaction. == Variations == If the protein is modeled with details about ../ProteinDomains, it is also possible to specify that the protein itself is cleaved. {{attachment:cleavage2_061115_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 The BioPAX representation of this binding could be a Biochemical Reaction object (e.g. Biochemical Reaction object with Interaction-Type = "de-phosphorylation", Participants = AP,A,P, Left = AP, and Right = A,P, where A, AP and B are physicalEntities.) AllanKuchinsky - 2006-11-17 03:28:19   Rendering of the phosphorylated species could be handled via the current vizmapper functionality, mapping an attribute signifying phosphorylation to a Node label, Node color, and Node line type.  Possible minor enhancements to the vizmapper and renderer may be needed to support values of "no border" and "no node color". ---- AllanKuchinsky - 2006-11-28 05:11:31   Actually, there may not be a 1-1 mapping between nodes in the model and nodes in the view.  In the topmost figure, is node3 (unphosphorylated A) only implicit in the view?  If that is the case, should node3 be only implicit in the model, as well?  But what if node3 is involved in a subsequent interaction?  How is that currently represented in MIMs?   ---- AllanKuchinsky - 2006-11-28 05:17:37   It appears as if cleavage between domains is a new use case for GroupAPI and may require extensions to the group model, as well as changes to the view.  I will write this up as a use case for GroupAPI. ---- AllanKuchinsky - 2006-11-29 04:25:22   Per cleavage between domains (and discussion with Scooter Morris), we might want to introduce the context of a 'site' for a CyNode, which could be used to represent cleavage sites, splice junctions, and other sub-node entities.  In the model, this could be implemented via the Group, each 'site' being a child of the group.  In the view, this could be represented as a 1-pixel wide rectangle adjacent to the border of the node, or perhaps a 1-pixel square rectangle at a point on the node.   This may constitute a re-invention of the construct of a 'port' in the Cytoscape context.