Paper Info
Title
Systems biology graphical notation markup language (SBGNML) version 0.3.
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.
Year
DOI
Venue
2020
10.1515/jib-2020-0016
JOURNAL OF INTEGRATIVE BIOINFORMATICS
Keywords
DocType
Volume
biological process diagrams,network biology,pathway diagram,SBGN,systems biology,visualization
Journal
17
Issue
ISSN
Citations 
2-3
1613-4516
0
PageRank 
References 
Authors
0.34
0
9
Name
Order
Citations
PageRank
Frank Bergmann124521.86
Tobias Czauderna216715.54
Ugur Dogrusoz321320.36
Adrien Rougny400.68
Andreas Dräger529222.16
Vasundra Toure612.74
Alexander Mazein7185.32
Michael L. Blinov819318.13
Augustin Luna9577.87