Translation of SBGN maps : Process Description to Activity Flow

Vogt, Torsten; Czauderna, Tobias; Schreiber, Falk

Translation of SBGN maps : Process Description to Activity Flow

Files

Vogt_0-395337.pdf(3.72 MB)

Date

2013

Authors

Vogt, Torsten

Czauderna, Tobias

Schreiber, Falk

Publication type

Journal article

Publication status

Published

Published in

BMC Systems Biology ; 7 (2013). - 115. - ISSN 1752-0509. - eISSN 1752-0509

Abstract

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).

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.

Subject (DDC)

004 Computer Science

Cite This

ISO 690

VOGT, Torsten, Tobias CZAUDERNA, Falk SCHREIBER, 2013. Translation of SBGN maps : Process Description to Activity Flow. In: BMC Systems Biology. 7, 115. ISSN 1752-0509. eISSN 1752-0509. Available under: doi: 10.1186/1752-0509-7-115

BibTex

@article{Vogt2013Trans-37543,
  year={2013},
  doi={10.1186/1752-0509-7-115},
  title={Translation of SBGN maps : Process Description to Activity Flow},
  volume={7},
  issn={1752-0509},
  journal={BMC Systems Biology},
  author={Vogt, Torsten and Czauderna, Tobias and Schreiber, Falk},
  note={Article Number: 115}
}

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