Use Case Name : ../SpeciesDegradation

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe the possibility that a protein is degraded as part of a ../StoichiometricConversion.

Step-by-Step User Action

  1. User specifies a protein to be degraded
  2. User specifies a ../StoichiometricConversion with this protein

  3. User specifies the result of the conversion is degradation
  4. User specifies the evidence for this relationship

Visual Aides

The Kohn notation for degradation is the following:


An example of the degradation symbol used as the result of a conversion follows:


The color in this example is convention, and is not an essential element in the notation.

Requirements for Cytoscape



This is a fairly common reaction.

Other Examples


Shared ../MimEditorUseCaseComments

In the context of a ../StoichiometricConversion, the BioPax representation would basically be the same as any other ../StoichiometricConversion, except that the degradation products would be described as small molecules, which would not be used in subsequent reactions.

AllanKuchinsky - 2007-01-22 05:15:47

Is there the need for special 'constant' Node(s) in Cytoscape to represent constructs like degradation?  Are there special semantics associated with degradation 'nodes', e.g. would one ever want to assign attributes to a particular degradation 'node'?

Molecular_Interaction_Maps/SpeciesDegradation (last edited 2009-02-12 01:03:30 by localhost)

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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