Molecular_Interaction_Maps/BooleanLogic

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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.

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.

Requirements for Cytoscape

TBD

Importance

The importance of this feature is uncertain. It is certainly a mechanism that has been used in many maps. On the other hand, most cases can be represented with some combination of contigencies (e.g. ../ShowInhibition, ../ShowNecessity)

Variations

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

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

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

Other Examples

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

Comments

Shared ../MimEditorUseCaseComments

BioPax representation TBD

AllanKuchinsky - 2007-01-19 03:24:53

At the model level, we might represent this as hyperedges whose ConnectorNodes have a specific NODE_TYPE, 'AND', 'OR', 'NOT'? At the view level, this might require something akin to a 'macro' that rendered a set (Group?) of hyperedges and ConnectorNodes as a grid of AND/OR notations.

Are we in effect borrowing the construct of a 'gate' from CAD systems? Should we consider introducing this construct into Cytoscape, possibly as a layer of abstraction built from Hyperedges and Groups?

MiritAladjem - 2007-02-01 08:15:58

Yes, we are thinking about the Booleans in terms of CAD gates.

vicce001 - 2007-02-28 11:19:32

whats the definition of booleanlogic