Cytoscape Wiki|
← Revision 6 as of 2006-11-17 19:14:44
Size: 3633
Comment: Using a more descriptive name
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← Revision 7 as of 2006-11-17 19:17:14 →
Size: 3470
Comment:
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| == Comments == | == Variations == |
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== Comments == Shared ../MimEditorUseCaseComments |
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The basic Kohn notation does not include a direct mechanism for attaching evidence to a particular reaction. In some of the eMims, we have added a text element A1, which can be subsequently linked to annotation information. |
Use Case Name : ../NonCovalentBinding |
For Feature : MIM Editor |
Editors: DavidKane |
Summary
A user wants to describe the possibility that two proteins can bind into a complex.
Step-by-Step User Action
- User specifies a protein to be involved in the interaction
- User specifies another protein to be involved in the interaction
- User specifies that there is a binding relationship between the two
- User specifies the evidence for this relationship
Visual Aides
The Kohn notation for this binding is the following:
attachment:simplebinding1a_061113_dwk.png
Requirements for Cytoscape
Best mapped to a group. A and B are connected and are part of the group. The edge might be a new node type. The visualization of the Kohn notation would require changes to the rendered and the vizmapper.
Importance
This is a basic building block of the Kohn notation.
Other Examples
Variations
A protein can be involved in more than one interaction. A protein can appear in a particular MIM once, and only once. If a protein is involved in additional reactions, then additional edges are added for each reaction.
attachment:simplebinding2a_061113_dwk.png
The layout rules for the edges for bindings require that they be horizontal or vertical, and may have any number of right angles. The edges may cross other edges at right angles.
Comments
Shared ../MimEditorUseCaseComments
The BioPAX representation of this binding could be a Conversion Object, i.e. with Participants = A,B, AB, Left = A,B, Right=AB, where A and B are Proteins, but AB is a complex with components A and B )