Browsing by Author "Bergmann, F. T."

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    Software support for SBGN maps: SBGN-ML and LibSBGN
    (Oxford University Press, 2012) Iersel, Martijn P. van; Villéger, A. C.; Czauderna, T.; Boyd, S. E.; Bergmann, F. T.; Luna, A.; Demir, E.; Sorokin, A.; Dogrusoz, U.; Matsuoka, Y.; Funahashi, A.; Aladjem, M. I.; Mi, H.; Moodie, S. L.; Kitano, H.; Le novère, N.; Schreiber, F.
    Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. © The Author(s) 2012. Published by Oxford University Press.
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    Systems biology graphical notation markup language (SBGNML) version 0.3
    (De Gruyter, 2020) Luna, A.; Bergmann, F. T.; Czauderna, T.; Doğrusöz, Uğur; Rougny, A.; Dräger, A.; Touré, V.; Mazein, A.; Mazein, M. L.
    This document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, modelers, and computer scientists. SBGN aims at representing networks of biochemical interactions in a standard, unambiguous way to foster efficient and accurate representation, visualization, storage, exchange, and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. SBGN is defined neutrally to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language. The notable changes from the previous version include the addition of attributes for better specify metadata about maps, as well as support for multiple maps, sub-maps, colors, and annotations. These changes enable a more efficient exchange of data to other commonly used systems biology formats (e. g., BioPAX and SBML) and between tools supporting SBGN (e. g., CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA). More details on SBGN and related software are available at http://sbgn.org. With this effort, we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.