## page was renamed from Molecular Interaction Maps/EnzymaticStimulationInTrans ## page was renamed from EnzymaticStimulationInTrans ## 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''' : ../InTrans || || '''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 specify ''in trans'', i.e. that a species is involved in an enzymatic or binding activity with another copy of the same species == 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 an existing enzymatic stimulation or binding activity 1. User specieis that the activity is ''in trans'' 1. User optionally specifies the evidence for the relationship As an alternative to modifying an existing relationship, this use case might be viewed as creating a different relationship in the first place, e.g. 1. User specifies a species to be the enzymatic stimulator 1. User specifies a reaction to be stimulated involving the same species 1. User specifies that there is a stimulation ''in trans'' relationship 1. User optionally specifies the evidence for the relationship == Visual Aides == ## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) The Kohn notation for enzymatic stimulation in trans is the following: {{attachment:intrans1_061121_dwk.png}} This notation can be used to modify the edges for ../NonCovalentBinding or ../EnzymaticStimulation {{attachment:intrans2_061121_dwk.png}} {{attachment:intrans4_061121_dwk.png}} An example using this notation for ../EnzymaticStimulation follows: {{attachment:intrans5_061121_dwk.png}} In this example, a copy of protein A, catalyzes the phosphorylation of another copy of protein A. The following example uses intrans for a ../NonCovalentBinding relationship: {{attachment:intrans3_061121_dwk.png}} In this example, a copy of protein A, binds a domain 1 to another copy of protein A at domain 2. == 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") Assuming that this can use the same approach that is used for ../ShowInhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation in trans), node2: A, node3: A 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 a fairly common occurance in the models. == Variations == An earlier version of the notation uses small circles instead of the slashes. This earlier notation does not need to be supported. {{attachment:enzymaticstimulationintrans1_061115_dwk.png}} {{attachment:enzymaticstimulationintrans2_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 This is a special case of an ../EnzymaticStimulation. It is intended to clarify that more than one copy of a particular protein is involved in the interaction. This could be modeled in BioPAX as a Catalysis object (e.g. Catalysis object with participants = a Biochemical Reaction object and a enzyme A, Controlled = the Biochemical Reaction object (a reaction in trans as defined in "in trans reactions"cannot communicate that is specifically a covalent phosphorylation reaction, Controller=A, Control-Type = Activation, and Direction = IRREVERSIBLE-LEFT-TO-RIGHT) AllanKuchinsky - 2007-01-20 04:29:49 model level requires new Edge type, as does view level should there be a 'special case' of Groups in Cytoscape to represent 'sub-molecular' entities, such as domains, splice sites, etc. Is there a common enough set of semantics to justify this? Do we ever need to represent phenomena at the level of a sequence. MiritAladjem - 2007-02-01 09:02:47 Allan, in response to your second queston, we anticipate that people will want to use the Kohn annotation to depict interactins within molecules. We already have some people collaborating with us to develop such maps. It will be good to support this effort by allowing sub-molecular interactions. The level of a sequence might be a derivativce of sub-molecules.