Cytoscape WikiUse Case Name : ../CompoundBinding |
For Feature : ../MIMEditor |
Editors: DavidKane |
Summary
A user wants to describe the possibility that a species (protein or complex) binds with another species (protein or complex).
Step-by-Step User Action
- User specifies a species to be involved in the interaction
- A dot on the edge describing the complex indicates that it is used in a further reaction
- User specifies another species to be involved in the interaction
- User specifies that there is a binding relationship between the species
- User specifies the evidence for this relationship
Visual Aides
The Kohn notation for this binding is the following. In this example, a species (the complex AB) binds to another species (protein C):
attachment:compoundbinding1_061113_dwk.png
Requirements for Cytoscape
Best mapped to a group. A and B are connected and are part of the group, and that group with C would be involved in a another 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 another basic building block of the Kohn notation. The concept of the result of a reaction being involved in subsequent reactions occurs repeatedly
Other Examples
Variations
A complex can be involved in more than one interaction. If a complex is involved in more than one interaction, the additional dots are placed on the edge for each reaction.
attachment:compoundbinding2_061113_dwk.png
The product of compound binding can be used in additional reactions, just as the results of ../NonCovalentBinding can.
attachment:compoundbinding3_061113_dwk.png
The product of two compound bindings can also be involved in a reaction with each other.
attachment:compoundbinding4_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 = AB, C, ABC, Left = AB,C, Right=ABC, where C is a Protein, AB is a Complex with components A and B, and ABC is a Complex with components AB,C)