Cytoscape WikiUse Case Name : SimpleBinding |
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:simplebinding1_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
Comments
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:simplebinding2_061113_dwk.png
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 )
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.