Publikation: Translation of SBGN maps : Process Description to Activity Flow
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2013
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BMC Systems Biology. 2013, 7, 115. ISSN 1752-0509. eISSN 1752-0509. Available under: doi: 10.1186/1752-0509-7-115
Zusammenfassung
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.
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VOGT, Torsten, Tobias CZAUDERNA, Falk SCHREIBER, 2013. Translation of SBGN maps : Process Description to Activity Flow. In: BMC Systems Biology. 2013, 7, 115. ISSN 1752-0509. eISSN 1752-0509. Available under: doi: 10.1186/1752-0509-7-115BibTex
@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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<dcterms:abstract xml:lang="eng">Background<br /><br />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.<br /><br />Results<br /><br />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).<br /><br />Conclusions<br /><br />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.</dcterms:abstract>
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