Molecular_Interaction_Maps/BooleanLogic

TableOfContents([2])

Summary

A wants to use the logical expressions AND or OR to describe the participants in a reaction.

Step-by-Step User Action

1. User specifies an existing contingency relationship (e.g. ../ProcessStimulation or ../ShowInhibition)

2. User specifies another species to be involved in that relationship
3. User specifies a logical operator (i.e. AND or OR)
4. User connects the species to the relationship using the logical operator
5. User optionally specifies the evidence for this reaction

Visual Aides

The AND notation uses converging edges to form an accute angle to indicate that all of the elements on the left, are required by the contigency relationship indicated by the arrowhead on the right.

attachment:booleannotation1_061117_dwk.png

The OR notation uses parallel edges to to indicate that all of the elements on the left, can independently have contigency relationship indicated by the arrowhead on the right.

attachment:booleannotation2_061117_dwk.png

Requirements for Cytoscape

TBD

Importance

TBD

Other Examples

The AND and OR notations can be combined, as in this example.

attachment:booleannotation3_061117_dwk.png

Some maps also use the following shorthand notation. This the shorthand notation for AND, it is the equivalent of the example above.

attachment:booleannotation4_061117_dwk.png

This the shorthand notation for OR, it is the equivalent of the example above.

attachment:booleannotation5_061117_dwk.png

This the shorthand notation that combined AND and OR, it is the equivalent of the example above.

attachment:booleannotation6_061117_dwk.png

Comments

Shared ../MimEditorUseCaseComments

BioPax representation TBD

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