Process Description Bricks
This page presents a collection of Process Description bricks. Please note that here we show general patterns, more complex cases are possible. For example metabolic reaction can include multiple substrate and products and more than one protein or complex can catalyze a reaction.
Metabolic network
Irreversible reaction. The substrate and the product of the biochemical reaction are represented by simple chemical glyphs. The substrate is connected to the process glyph by a consumption arc and the product is connected to the process by a production arc.
Catalysis: irreversible reacton. The enzyme catalyses an irreversible metabolic process which consumes substrate S1 and produces product P1. The enzyme is a represented as a macromolecule connected to the process glyph by a catalysis arc. The substrate and the product of the biochemical reaction are represented by simple chemical glyphs.
Catalysis: reversible reaction. In case of a reversible reaction, the separation substrate vs. product is relative and each metabolite can be seen an input or an output of this reaction depending on the direction.
IMPORTANT: Note that it is not clear which direction is favoured by the catalysis. Instead of presenting it as a reversible process, it is recommended showing direct and reverse reactions, both as irreversible processes.
IMPORTANT: Note that it is not clear which direction is favoured by the catalysis. Instead of presenting it as a reversible process, it is recommended showing direct and reverse reactions, both as irreversible processes.
Catalysis: multiple substrates and products. The enzyme catalyses an irreversible metabolic process which consumes two substrates S1 and S2 and produces two products P1 and P2.
Inhibition: irreversible metabolic reaction. The inhibitor, a proteins shown with a macromolecule glyph, is connected to the process glyph by an inhibition arc.
IMPORTANT: Please note that inhibition arcs in Process Descrition go to a process glyph and not directly to a micromolecule or a complex. Direct connections between activities are possible in the Activity Flow language.
IMPORTANT: Please note that inhibition arcs in Process Descrition go to a process glyph and not directly to a micromolecule or a complex. Direct connections between activities are possible in the Activity Flow language.
Signalling network
 SBGN-ML Newt |
Protein phosphorylation. A kinase protein catalyzes an irreversible reaction which consumes unphosphorylated protein X and ATP and produces phosphorylated protein X and ADP. Phosphorylated state is shown by "P" in the auxiliary glyph. All proteins involved are represented by macromolecule glyphs. |
SBGN-ML Newt |
Protein phosphorylation. A kinase protein catalyzes an irreversible reaction which consumes unphosphorylated protein X and ATP and produces phosphorylated protein X and ADP. Phosphorylated state is shown by "P" in the auxiliary glyph. Can also be acetilated "Ac", ubiquitinated "Ub" etc. All proteins involved are represented by macromolecule glyphs. |