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BY 4.0 license Open Access Published by De Gruyter June 22, 2020

Systems biology graphical notation markup language (SBGNML) version 0.3

Frank T. Bergmann ORCID logo , Tobias Czauderna ORCID logo , Ugur Dogrusoz ORCID logo , Adrien Rougny ORCID logo , Andreas Dräger ORCID logo , Vasundra Touré ORCID logo , Alexander Mazein ORCID logo , Michael L. Blinov ORCID logo and Augustin Luna ORCID logo EMAIL logo

Abstract

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.


Corresponding author: Augustin Luna, cBio Center, Department of Data Sciences, Dana–Farber Cancer Institute, Boston, 02215, MA, USA; and Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA, E-mail:

Received: 2020-04-01
Accepted: 2020-04-16
Published Online: 2020-06-22

© 2020 Frank T. Bergmann et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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