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← Revision 1 as of 2006-11-15 22:05:15 →
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Comment: Clarified that this use case only applies to binding reaction
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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 || | || '''Use Case Name''' : ../ShowCompetition || |
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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 |
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In this example, the protein A can be bound to either B or C, and that both reactions are competing to recruit A. 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: |
In this example, the protein A can be bound to either B or C, and that both reactions are competing to recruit A. |
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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: attachment:competition2_061115_dwk.png |
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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. |
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:
attachment:competition1_061115_dwk.png
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:
attachment:competition2_061115_dwk.png
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.
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
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.