Translation of SBGN maps: Process Description to Activity Flow

BMC Systems Biology

Falk Schreiber²  Tobias Czauderna³  Torsten Vogt¹ 

[1]Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany

[2]Clayton School of Information Technology, Monash University, Victoria 3800, Australia

[3]Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland OT Gatersleben, Germany

关键词: Activity Flow;    Process Description;    Translation;    SBGN;   

Others  :  1141964
DOI  :  10.1186/1752-0509-7-115

 received in 2013-04-26, accepted in 2013-10-23,  发布年份 2013

【 摘 要 】

Background

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.

Results

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 webcite).

Conclusions

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.

【 授权许可】

   
2013 Vogt et al.; licensee BioMed Central Ltd.

【 图 表 】

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