Use Case Name : ../StateCombination

For Feature : MIMEditor

Editors: DavidKane

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A user wants specify a condition that is the combination of two previously specified conditions. The two previous conditions may exist in separate species or within the same molecule.

Step-by-Step User Action

  1. User specifies a species to be combined
  2. User specifies another species to be combined
  3. User specifies that the two species are to be combined
  4. User optionally specifies the evidence for the relationship

Visual Aides

The combination is represented with an arrowless line between the two species:


State combinations can occur intramolecularly, for example, two different modifications on two different residues within the same molecule might be required for a specific activity. In the example below a phosphorylation reaction and an acetylation reaction are both required for stimulation:


Requirements for Cytoscape



This is of moderate importance. A situation in which a reaction is contingent upon several requirements is common in biology. Examples include enzymes that need to be modified on several residues (phoshphorylation, acetylation) in order to catalyze specific reactions, or molecules that need to bind several other molecues in an unspecified order to participate in a process.

Other Examples


Shared ../MimEditorUseCaseComments

AllanKuchinsky - 2006-11-21 14:58:17

Model: the example of phosphorylation/acetylation could be handled in the model using the same constructs as A--.--B

The user would need a way to specify the constraint that A and B must consist of phosphorylation and acetylation, or vice versa.  

How would the user specify the constraints?  What variety of constraints would we want to give the user?  The most straightforward case would be 'type checking' of the nodes and edges.  Is this sufficient for the majority of usage?  Do we need to supply a more general constraint handling mechanism and 'language'?

View: do we need a library of 'view' templates to handle views such as the phosphorylation/acetylation example?

MiritAladjem - 2007-02-01 09:27:16

Allan, in answer to your third question, in the Kohn annotation the depiction above is sufficient to determine that there are constraints.   In the example above, the node between the phosphorylated state of the molecule and the acetylated state of the molecule is the outcome of combining the two states. This is sufficient for the majority of cases.

In answer to the fourth question, yes, in a "MIM tool" it will be nice to have a library of commmon reactions such as covalent binding with the common agents such as phosphorylation, methylation etc.

Molecular_Interaction_Maps/StateCombination (last edited 2009-02-12 01:03:38 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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