Systems biology graphical notation markup language (SBGNML) version 0.3

Abstract

This document defines Version 0.3 Markup Language (ML) support for the Systems BiologyGraphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, mod-elers, 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 reuseof 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 primarilytowards allowing models to be encoded using XML, the eXtensible Markup Language. The notable changesfrom the previous version include the addition of attributes for better specify metadata about maps, as well assupport for multiple maps, sub-maps, colors, and annotations. These changes enable a more efficient ex-change of data to other commonly used systems biology formats (e. g., BioPAX and SBML) and between toolssupporting SBGN (e. g., CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA). More detailson SBGN and related software are available at http://sbgn.org. With this effort, we hope to increase theadoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biologicalknowledge in a precise and unambiguous manner.