Cytoscape WikiUse Case Name : Cleavage |
For Feature : MIM Editor |
Editors: DavidKane |
Summary
A user wants to describe the possibility that a covalent bond can be cleaved.
Step-by-Step User Action
- User specifies a covalent bond that is to be cleaved
- User specifies a species that acts to cleave the bond
- User specifies that there is a cleaving relationship between the two
- User optionally specifies the evidence for this relationship
Visual Aides
The Kohn notation for this binding is the following. The species that is cleaving the bond is on end of the edge. The other end of the edge goes across the bond that is being cleaved.
attachment:cleavage1_061115_dwk.png
The color in this example is convention, and is not an essential element in the notation.
Requirements for Cytoscape
This could be modeled as a hyperedge containing node1: Phtase (hyperedge attribute: enzyme), node2: phosphorylated A, node3: unphosphorylated A. The mapping might be different if it is a protein that is being cleaved. View: Use case for hyperedge view. Might require a new line type in Vizmapper.
Importance
This is important because it is a fairly common activity in the maps. In addition, it is an example of a reversal of another reaction.
Variations
If the protein is modeled with details about ProteinDomains, it is also possible to specify that the protein itself is cleaved.
attachment:cleavage2_061115_dwk.png
Other Examples
Comments
The BioPAX representation of this binding could be a Biochemical Reaction object (e.g. Biochemical Reaction object with Interaction-Type = "de-phosphorylation", Participants = AP,A,P, Left = AP, and Right = A,P, where A, AP and B are physicalEntities.)