IndirectControlProposal

- = Executive Summary =

To describe indirect control, such as indirect catalysis, you need to create an intermediate pathway object that represents the indirect steps. The only problem with this right now is that BioPAX Level 2 only allows a physical entity to be a controller, not pathway.

This is currently a requirement of the Institute of Bioinformatics

We propose to create a maintenance release of BioPAX Level 2 that would allow a pathway instance to be a controller in a control interaction.

- = Introduction =

Goals/Motivation/Requirements

 * Add the ability to describe indirect control, such as indirect catalysis

= Biological Questions / Use Cases =


 * 1) An example of an indirect catalysis:



The small triangles are control interactions and the small square is a conversion (biochemical reaction in this case). The black circle indicates a complex. The large object is the pathway that represents the indirect control event.

Description: Carbachol was added to cells, which led to an increase in PKD1 phosphorylation (through an unknown mechanism). Also, gf109203x can inhibit the activation of phosphorylation by Carbachol

(Image by Emek Demir, based on data courtesy of Cell Signaling Technologies)

= Proposed Implementation =


 * 1) Change the range on the CONTROLLER property in the control class from "physicalEntityParticipant" to "pathway or physicalEntityParticipant"

= Open Issues =


 * 1) None

= Backward Compatibility =


 * 1) This change is backwards compatible, since it only adds to the range of an existing property.

-

IndirectControlProposal/Discussion:Discuss this proposal.