Translation Rules

• Green: implemented
• Yellow: partly implemented
• Pink: not yet implemented

Inhibition

By Binding

SBGN-ML  Newt	SBGN-ML  Newt
A binds B to a complex, reducing concentration of B and stimulation of reaction D1 to D2, hence inhibiting the reaction D1 to D2

By Modification

SBGN-ML  Newt	SBGN-ML  Newt
A stimulates B1 to become B2, reducing concentration of B1 and stimulation of reaction C1 to C2, hence inhibiting the reaction C1 to C2

By Degradation

SBGN-ML  Newt	SBGN-ML  Newt
A dissociates into B and C. This decreases the concentration of A, and as A stimulated reaction D1 to D2, dissociation inhibits this reaction

Simple Control

Simple Negative Control

SBGN-ML  Newt	SBGN-ML  Newt
A inhibits a reaction of modification B to C, while B participates also in some other reaction

Simple Positive Control

SBGN-ML  Newt	SBGN-ML  Newt
A controls a reaction of modification B to C, while B also participates in some other reeactions

Simple Negative Control With Dead End

SBGN-ML  Newt	SBGN-ML  Newt
A inhibits a reaction of modification B to C, while B participates only in this reaction

Simple Positive Control With Dead End

SBGN-ML  Newt	SBGN-ML  Newt
A stimulates a reaction of modification B to C, while B participates only in this reaction

Translation Pattern

Self Stimulation

SBGN-ML  Newt	SBGN-ML  Newt
If some element controls reaction it also takes part as a substrate (self-stimulation or self-inhibition), then this control is not translated into a self-influence on AF diagram

Collapsing Equal Name Elements

SBGN-ML  Newt	SBGN-ML  Newt
If several PD elements have the same name, then translation collapses them into a single AF element with this name. Elements considered to be of the same name, if they have equal labels, even if their states are different. All influences on reactions these elements possesed are joined into the single new one.

Process Is A Positive Influence

SBGN-ML  Newt	SBGN-ML  Newt
Plain process without enzyme regulation is translated as a positive-influence

Source-And-Sinks

Control Over Sink

SBGN-ML  Newt	SBGN-ML  Newt
A sink takes role of outcoming metabolite in the simple control pattern, it should not be represented in Activity Flow diagram. B is included to AF diagram, even if it participates only in this reaction

Control Over Source

SBGN-ML  Newt	SBGN-ML  Newt
A source takes role of incoming metabolite in the simple control pattern, it should not be represented in Activity Flow diagram. In contrary to the source, C element is always included into AF diagram, even if it doesn't participate in other reactions