Learning SBGN

This is a brief introduction to the SBGN languages, and, in particular, we focus on the Process Description language as the currently most used language of the SBGN standard. The SBGN dictionary will help to align biological concepts with graphical expressions, and redrawing a small example diagram will help with a quick start.

The three languages of SBGN

There are three complementary languages in SBGN: Activity Flow (AF), Process Description (PD) and Entity Relationship (ER).

Representations

In the figure the same biological system is shown in different representations depending on the concepts used to describe it (Le Novère, 2015, doi:10.1038/nrg3885). Note the same set of four proteins in all cases. In Process Description ELK1 shown in three differents states, with ELK1 sumoylation (SUMO) and phosphorylation (P) processes.

Next, to avoid any confusion, we concentrate only on the Process Description (PD) language.

Process in SBGN PD

The process glyph is the key element for understanding of the SBGN PD language:

Process

Reading a PD diagram is much simpler if it is seen as a collection of interconnected processes. Represented in PD, a biological process includes 1) incoming consumption link(s) to the process, 2) production link(s) from the process, and often 3) regulatory link(s) to the process, for example stimulation or inhibition.

example

SBGN PD dictionary

Here are some illustrations of how biological concepts such as metabolic reaction or complex formation can be reflected in the SBGN Process Description language (Junker et al., 2012, doi:10.1016/j.tibtech.2012.08.003). An extended collection of PD patterns is available at the SBGN briks page.


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
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 macromolecules.

iNOS pathway example

After simply redrawing the following example you will be much more familiar with how the SBGN PD language works. This was proved to be very useful in various tutorials and university courses. The example pathway diagram is comparatively small but includes many types of biological processes and the corresponding elements of the graphical notation.

iNOS

Downloads:PNGSVGSBGN-MLNewt

The diagram can be redrawn in any application that supports the required shapes, for example, in PowerPoint, InkScape or Adobe Illustrator. For that the available templates can be used. In GraphML format the diagram can be developed in yEd Graph Editor (desktop application) that since version 3.17.1 provides a palette section for SBGN.

To build the diagram and generate SBGN-ML file, a dedicated software should be used, for example Newt (online editor) or SBGN-ED add-on for VANTED (desktop application). At the end, to check that your diagram is correct or to see what went wrong you can use the validation tool of the SBGN-ED.

Tips for creating diagrams in SBGN

This section is based on the educational paper by Touré and co-authors Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation (Touré et al., 2018, doi:10.1371/journal.pcbi.1005740).

Tip 1: Know the message your network should convey. This will help you choose what to omit, what to represent, and how to represent it.

Tip 2: Know your audience. Different readers perceive different messages. Ask yourself: What do they know and what do they not know? What are they interested in?

Tip 3. Choose the right SBGN language. Design your map in a reasonable level of detail.

Tip 4. Define components and interactions in the network. Map the components to SBGN glyphs and build the connectivity of your network by selecting the appropriate arcs to link the components.

Tip 5. Select the right level of granularity for your map. Be as specific as you can without diluting your message: important parts of your network should stand out to the readers.

Tip 6. Design your SBGN map. Start by creating the components and their interactions then add necessary information in respect to Tip 5.

Tip 7. Beautify your SBGN map. Your map should be visually appealing to your audience if you expect them to look into the details.

Tip 8. Manage your SBGN map and its content. Save your map in different formats to facilitate the sharing and reusability of your work.

Tip 9. Link the original data to your SBGN map. When publishing your work, link the SBGN visualisation to your original data (i.e. model, data set).

Tip 10. Seek help from the SBGN community. Request feedback and ask questions using the sbgn-discuss mailing list. Don’t be shy!

SBGN PD Reference Card

SBGN PD Reference Card

Reading list

  1. Le Novère et al. The Systems Biology Graphical Notation. Nat Biotechnol. 2009. doi:10.1038/nbt.1558
  2. Touré et al. Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Computat Biol. 2018. doi:10.1371/journal.pcbi.1005740
  3. Le Novère. Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet. 2015. doi:10.1038/nrg3885

Additional materials

Please review example diagrams and additional tutorial materials that can be found in the Education Resource repository. For more advanced questions please use FAQ, in particular FAQ Process Description.


For questions and comments please contact the SBGN editors team at
sbgn-editors@googlegroups.com