Cytoscape Wiki|
← Revision 1 as of 2006-11-15 22:05:15
Size: 3561
Comment:
|
← Revision 2 as of 2006-11-15 22:07:52 →
Size: 3683
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 34: | Line 34: |
|
attachment:competition1_061115_dwk.png |
|
| Line 35: | Line 37: |
|
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. |
| Line 52: | Line 52: |
|
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 |
|
| Line 54: | Line 58: |
| attachment:competition3_061115_dwk.png |
Summary
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.
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 reactions
- User specifies another 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
Other Examples
Comments
Shared MimEditorUseCaseComments
We are unsure how to best model competition under BioPAX.