Systems biology graphical notation markup language (SBGNML) version 0.3

  • 1 BioQUANT/COS, Heidelberg University, INF 267, Heidelberg, Germany
  • 2 Faculty of Information Technology, Monash University, Melbourne, Australia
  • 3 Computer Engineering Department, Bilkent University, 06800, Ankara, Turkey
  • 4 i-Vis Research Lab, Bilkent University, 06800, Ankara, Turkey
  • 5 Biotechnology Research Institute for Drug Discovery, AIST, 135-0064, Tokyo, Japan
  • 6 Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 169-8555, Tokyo, Japan
  • 7 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), 72076, Tübingen, Germany
  • 8 Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
  • 9 German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, 72076, Germany
  • 10 Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
  • 11 Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg
  • 12 Center for Cell Analysis and Modeling, UConn Health, Farmington, USA
  • 13 cBio Center, Department of Data Sciences, Dana–Farber Cancer Institute, 02215, Boston, USA
  • 14 Department of Cell Biology, Harvard Medical School, Boston, USA
  • 15 European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 69007, Lyon, France

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.

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The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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