Diff for "Molecular_Interaction_Maps/StoichiometricConversion"

TableOfContents([2])

Summary

A user wants to describe the possibility that one or more species are converted into another species or collection of species through a stoichiometric process.

Step-by-Step User Action

1. User specifies a species or collection of species to be converted
2. User specifies the species or collection of species that that results from the conversion
3. User specifies that there is a stoichiometric conversion process from source species to the products of the conversion
4. User optionally specifies the evidence for this relationship

Visual Aides

The Kohn notation for this binding is the following:

attachment:stoichiometricconversion1_061115_dwk.png

If a conversion results in more than one product, then this is represented with the following notation:

attachment:stoichiometricconversion2_061115_dwk.png

Note that the angled lines here when representing multiple products from a stochiometric conversion are one of the few places where edges are not at right angles. The angle where the reaction splits to the competing products or sources, should be less than 90º. This can be difficult from a layout perspective, and so the following form of the notation is usually easier to use:

attachment:stoichiometricconversion3_061115_dwk.png

Requirements for Cytoscape

Could be modeled as a group, or perhaps more simply as a node and two edges. Not clear how the model would need to be adjusted if there are more than one input or product. Might require a new line type in Vizmapper.

Importance

Stochiometric conversion is fairly common on its own. In addition, the use cases of Degradation and Transport are in fact, special cases of Stochiometric conversion.

Variations

The following example illustrates a pair of common scenarios associated with this use case. First, is that a species (i.e. a catalyst), may be both an input and a product of the conversion. Second, the species that is the input into the conversion can be a complex.

attachment:stoichiometricconversion4_061115_dwk.png

There can be more than two products from a reaction. If that is the case, additional edges emanate from the vertex, but the outer angles should still be less than 90ºapart.

attachment:stoichiometricconversion5_061115_dwk.png

It is also possible to have more than one input into a stoichiometric conversion. The notation for this is the following:

attachment:stoichiometricconversion6_061115_dwk.png

An alternative to this notation for representing multiple inputs is to use StateCombination:

attachment:stoichiometricconversion7_061115_dwk.png

Enzymatic catalysis involves the stoichiometric conversion of the reagents to the products with regeneration of the enzyme. The example below shows the enzyme E catalyzing the addtion of a hydroxyl group OK onto protein S:

attachment:stoichiometricconversion8_061115_dwk.png

Other Examples

Comments

Shared MimEditorUseCaseComments

The BioPAX representation of this binding could be a Biochemical Reaction object that has participants: A,A, and AA, left = A,A, and right=AA. AA = Conversion object (child of Interaction class), e.g. Conversion object with Participants=A,B, Left=A, Right=B, where A and B are physicalEntities. PageComment2