Translation of SBGN maps: Process Description to Activity Flow

BMC Systems Biology
Torsten VogtFalk Schreiber

Abstract

The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration. To solve this problem we define translations of SBGN PD maps into the more abstract SBGN AF maps. We present a template-based translation which allows the user to focus on different aspects of the underlying biological system. We also discuss aspects of laying out the AF map and of interactive navigation between both the PD and the AF map. The methods developed here have been implemented as part of SBGN-ED ( http://www.sbgn-ed.org). SBGN PD maps become much smaller and more manageable when translated into SBGN AF. The flexible translation of PD into AF and related interaction methods are an initial step in translating the different SBGN languages and open the path to future research for translation methods between other SBGN languages.

References

Aug 12, 2009·Nature Biotechnology·Nicolas Le NovèreHiroaki Kitano
Apr 20, 2010·Trends in Plant Science·Astrid JunkerHelmut Bäumlein
Jul 16, 2010·Bioinformatics·Tobias CzaudernaFalk Schreiber
Aug 28, 2012·Bioinformatics·Finja BüchelAndreas Zell
Nov 13, 2012·BMC Systems Biology·Hendrik RohnFalk Schreiber

Citations

Dec 26, 2013·BioMed Research International·Antonina V TrukhinaAlexander F Smirnov
Jul 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·Liang ZhaoPeter Koopman
Jun 17, 2016·BMC Systems Biology·Adrien RougnyLoïc Paulevé
May 14, 2020·Bioinformatics·Sara Sadat AghamiriAnna Niarakis
Mar 24, 2021·Briefings in Bioinformatics·Adrien RougnyAlexander Mazein

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