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.
Highlights
The Systems Biology Graphical Notation (SBGN) aims to standardize the graphical/visual representation of bio- 2 chemical and cellular processes (Czauderna and Schreiber, 2017; Junker et al, 2012; Novère et al, 2009; Touré et al, 32018)
We assume that for diagram editing software to communicate a model encoded in SBGN, 6 the program will have to translate its internal data structures to and from SBGNML, use a suitable transmission 7 medium and protocol, and to provide any further necessary infrastructure
We expound on the various data types and constructs defined in this package, in Section 3 on page 24; we provide 8 complete examples of using the constructs in sample SBGN models
Summary
■ The SBGN AF “perturbation” glyph, which was an activity node, has been deprecated and is a unit of 1 information. We assume that for diagram editing software to communicate a model encoded in SBGN, 6 the program will have to translate its internal data structures to and from SBGNML, use a suitable transmission 7 medium and protocol, and to provide any further necessary infrastructure. These issues are outside the 8 scope of this document. The software EscherConverter provides an SBGN viewer and a 13 bidirectional converter for metabolic maps in JSON format and SBGNML (King et al, 2015).
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