Choice of SBGN language

Introduction to SBGN languages

SBGN offers three languages adjusted to different applications, namely the Process Description (PD) language, the Entity Relationship (ER) language and the Activity Flow (AF) language [1, 2]. Le Novère reviews the advantages of each language with regard to the different views of systems biology on biological processes and relationships [3]. In brief, AF maps are directed and sequential, but not mechanistic and therefore suitable for logic models, ER maps are directed and mechanistic, but not sequential and therefore suitable for signalling pathways, whereas PD maps are directed, sequential and mechanistic. PD maps are wiedely used, especially for metabolic reactions.

Choice of appropriate SBGN language

While creating the SBGN map for the Bachmann model, we were oriented towards the tips for SBGN creation by Touré et al. [4], who also comment on the choice of the right SBGN language. The Bachmann model is a Ordinary Differential Equation (ODE) model. As mentioned before (Chapter SBGN Maps), the authors use a process diagram to vizualize the model in the publication. Accordingly, we choose the PD language for the SBGN map of the Bachmann model, because the PD map can be organized directed, sequential and mechanistic. Furthermore, the PD language allows us to show the process of the different entities in the Bachmann model and also the influence of the entities on others at the right level of granularity. PD maps are common in the field of biochemistry and in the representation of ODE models [5, 6].

PD language specification

The latest specification of the PD language when creating the SBGN map is: Process Description language Level 1 Version 2.0, published in [2].

SBGN-ML specification

The Systems Biology Graphical Notation Markup Language (SBGN-ML) is an open, machine-readable exchange format for SBGN maps [7]. SBGN-ML allows the collaborative and platform independent work on existing SBGN maps. The latest specification is: Systems biology graphical notation markup language (SBGNML) version 0.3, published in [8].

References

[1] Novère, N., Hucka, M., Mi, H. et al. The Systems Biology Graphical Notation. Nat Biotechnol 27, 735–741 (2009). https://doi.org/10.1038/nbt.1558

[2] Rougny, A., Touré, V., Moodie, S. et al. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. 16, 20190022 (2019). https://doi.org/10.1515/jib-2019-0022

[3] Le Novère, N. Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet 16, 146–158 (2015). https://doi.org/10.1038/nrg3885

[4] Touré, V., Le Novère, N., Waltemath, D. et al. Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation. PLoS Comput Biol 14, e1005740 (2018). https://doi.org/10.1371/journal.pcbi.1005740

[5] Vogt, T., Czauderna, T. & Schreiber, F. Translation of SBGN maps: Process Description to Activity Flow. BMC Syst Biol 7, 115 (2013). https://doi.org/10.1186/1752-0509-7-115

[6] Rougny, A., Froidevaux, C., Calzone, L. et al. Qualitative dynamics semantics for SBGN process description. BMC Syst Biol 10, 42 (2016). https://doi.org/10.1186/s12918-016-0285-0

[7] van Iersel, M.P., Villéger, A. C., Czauderna, T. et al. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 28, 2016-2021 (2012). https://doi.org/10.1093/bioinformatics/bts270

[8] Bergmann, F. T. et al. Systems biology graphical notation markup language (SBGNML) version 0.3. Journal of Integrative Bioinformatics 17, 20200016 (2020). https://doi.org/10.1515/jib-2020-0016