Use Case Name : SimpleBinding

For Feature : MIM Editor

Editors: DavidKane

TableOfContents([2])

Summary

A user wants to describe the possibility that two proteins can bind into a complex.

Step-by-Step User Action

  1. User specifies a protein to be involved in the interaction
  2. User specifies another protein to be involved in the interaction
  3. User specifies that there is a binding relationship between the two
  4. User specifies the evidence for this relationship

Visual Aides

The Kohn notation for this binding is the following:

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.

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.

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Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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