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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

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ISSN
1613-4516
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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Adrien RougnyORCID iD: https://orcid.org/0000-0002-2118-035X / Vasundra TouréORCID iD: https://orcid.org/0000-0003-4639-4431 / Stuart Moodie / Irina BalaurORCID iD: https://orcid.org/0000-0002-3671-895X / Tobias Czauderna ORCID iD: https://orcid.org/0000-0002-1788-9593 / Hanna BorlinghausORCID iD: https://orcid.org/0000-0002-5410-6877 / Ugur DogrusozORCID iD: https://orcid.org/0000-0002-7153-0784 / Alexander MazeinORCID iD: https://orcid.org/0000-0001-7137-4171
  • European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
  • Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
  • Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, Pushchino, Moscow Region, 142290, Russia
  • orcid.org/0000-0001-7137-4171
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Andreas DrägerORCID iD: https://orcid.org/0000-0002-1240-5553
  • Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), 72076 Tübingen, Germany
  • Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
  • German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
  • orcid.org/0000-0002-1240-5553
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Michael L. BlinovORCID iD: https://orcid.org/0000-0002-9363-9705 / Alice Villéger / Robin HawORCID iD: https://orcid.org/0000-0002-2013-7835 / Emek Demir
  • Computational Biology Program, Oregon Health and Science University, Portland, Oregon, USA
  • Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, Oregon, USA
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Huaiyu MiORCID iD: https://orcid.org/0000-0001-8721-202X / Anatoly SorokinORCID iD: https://orcid.org/0000-0002-0047-0606 / Falk Schreiber
  • Faculty of Information Technology, Monash University, Melbourne, Australia
  • Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Augustin LunaORCID iD: https://orcid.org/0000-0001-5709-371X
Published Online: 2019-06-13 | DOI: https://doi.org/10.1515/jib-2019-0022

Abstract

The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).

Keywords: biological network; circuit diagram; SBGN; standard; systems biology; visualisation

About the article

Received: 2019-03-31

Revised: 2019-05-01

Accepted: 2019-05-21

Published Online: 2019-06-13


Citation Information: Journal of Integrative Bioinformatics, 20190022, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2019-0022.

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© 2019, Adrien Rougny et al., published by Walter de Gruyter GmbH, Berlin/Boston. This work is licensed under the Creative Commons Attribution 4.0 Public License. BY 4.0

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