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## page was renamed from Molecular Interaction Maps/Competition ## page was renamed from Competition |
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|| '''Use Case Name''' : Competition || || '''For Feature''' : Self:MIMEditor || |
|| '''Use Case Name''' : ../ShowCompetition || || '''For Feature''' : [[MIMEditor]] || |
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| [[TableOfContents([2])]] | <<TableOfContents([2])>> |
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| A user wants to describe the possibility that a species is involved in two or more reactions, and that these reactions are in competition for recruiting that species. | A user wants to describe the possibility that a species is involved in two or more binding reactions, and that these reactions are in competition for recruiting that species. |
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1. User specifies a species in that first reaction that will recruiting by the competing reactions 1. User specifies another reaction involving the species being recruited by both |
1. User specifies a species in that first reaction that will recruiting by the competing binding reactions 1. User specifies another binding reaction involving the species being recruited by both |
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| attachment:competition1_061115_dwk.png | {{attachment:competition1_061115_dwk.png}} |
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| attachment:competition2_061115_dwk.png | {{attachment:competition2_061115_dwk.png}} |
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{{attachment:competition3_061115_dwk.png}} Competition can also occur with ../CovalentBinding, in which case similar notation is used, but with the double-line used for ../CovalentBinding, as in this example: {{attachment:competition4_061121_dwk.png}} |
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| Shared MimEditorUseCaseComments | Shared ../MimEditorUseCaseComments |
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This typically is only modeled for noncovalent binding, however, the model has been occassionally used for covalent binding reactions as well. ---- AllanKuchinsky - 2006-12-11 03:21:31 At the model level, Should the competing reactions be represented by a Group, with the recruited species as the left side of the 'composite' reaction? Might we approach this via analogy to a set protein isoforms, one if which participates in a reaction under certain conditions? At the view level, would we need to show a less than 90-degree angle at the intersection of outgoing edges, i.e. an angle of pi/2*n, where n=number of competing elements? In the second variation, what is meant by the term "node"? Is it referring to the dot? ---- MiritAladjem - 2006-12-13 12:40:20 Allan, thank you for the comment. Regarding the first question, in the example above and in the first two variations the object on the left has the potential to form a group with either one of the two objects on the right. Regarding the third question, yes node=dot in the paragraph describing the second example. |
<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>
Summary
A user wants to describe the possibility that a species is involved in two or more binding reactions, and that these reactions are in competition for recruiting that species.
Step-by-Step User Action
- User specifies a reaction that will be one of those competing
- User specifies a species in that first reaction that will recruiting by the competing binding reactions
- User specifies another binding reaction involving the species being recruited by both
- User optionally specifies the evidence for this competition
Visual Aides
An example of the Kohn notation for this reaction follows:
In this example, the protein A can be bound to either B or C, and that both reactions are competing to recruit A.
Requirements for Cytoscape
TBD
Importance
This a fairly frequent occurrence in the maps, although it is not necessary to support both variations of the layout immediately. The second of the two variants above is the more important version to support.
Variations
The angle where the reaction splits to the competing participants, should be less than 90º. This can be difficult from a layout perspective, and so the following form of the notation is usually easier to use:
Each specific reaction can be involved in subsequent reactions. In addition, it is possible for the reaction to specify that either is a possibility. In this example, if the complex AB were necessary, then the node next to B would be used. If the complex AC were necessary, then the node next to C would be used. If either AB or AC could be used in a reaction, then the node next to A would be used.
Competition can also occur with ../CovalentBinding, in which case similar notation is used, but with the double-line used for ../CovalentBinding, as in this example:
Other Examples
Comments
Shared ../MimEditorUseCaseComments
We are unsure how to best model competition under BioPAX.
This typically is only modeled for noncovalent binding, however, the model has been occassionally used for covalent binding reactions as well.
AllanKuchinsky - 2006-12-11 03:21:31
At the model level, Should the competing reactions be represented by a Group, with the recruited species as the left side of the 'composite' reaction? Might we approach this via analogy to a set protein isoforms, one if which participates in a reaction under certain conditions?
At the view level, would we need to show a less than 90-degree angle at the intersection of outgoing edges, i.e. an angle of pi/2*n, where n=number of competing elements?
In the second variation, what is meant by the term "node"? Is it referring to the dot?
MiritAladjem - 2006-12-13 12:40:20
Allan, thank you for the comment.
Regarding the first question, in the example above and in the first two variations the object on the left has the potential to form a group with either one of the two objects on the right.
Regarding the third question, yes node=dot in the paragraph describing the second example.