SBGN bricks

SBGN bricks are defined as the recurring biological paterns reflected in the SBGN languages: metabolic reaction, catalysis, inhibition, protein phosphorylation, complex formation, transcription, translation etc. (Junker et al., 2012, doi:10.1016/j.tibtech.2012.08.003). SBGN bricks present a tamplate-based approach that allows to simplify learning SBGN and to start applying the standard without necesserily being familiar with all the specifications. The dictionary of SBGN bricks aligns biological concepts with their graphical expressions in SBGN languages.

The example bricks are developed using SBGN-ED add-on of VANTED editor. All the bricks are available for downloading in SBGN-ML format and can be opened online in Newt editor.

Process Description

This section 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 processes


SBGN-MLNewt
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.

SBGN-MLNewt
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.

SBGN-MLNewt
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.

SBGN-MLNewt
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.

SBGN-MLNewt
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.


Signalling processes


SBGN-MLNewt
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-MLNewt
Protein phosphorylation. A kinase protein catalyzes an irreversible reaction which consumes unphosphorylated protein X and ATP and produces phosphorylated protein X and ADP. All proteins involved are represented by macromolecule glyphs. State variable auxiliary glyphs are used to indicate the phosphorylation state: "P@Y701" means "phosphorylated at tyrosine 701" (one-letter amino acid code). Instead of empty state, "@Y701" without "P" can be used to indicate the position. ATP and ADP are represented as simple chemicals.

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