Logo


WHAT IS SBGN
SPECIFICATIONS
SOFTWARE
EVENTS
FAQ
HOW TO CITE
ABOUT
CONTACT

Learning SBGN
Examples
Reference Cards
Published Maps
Symbol Highlights
Figure to SBGN
Competition
Development Wiki

About

The mission of the SBGN project is to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word.

Get involved

Regardless of your experience or involvement level, we value your ideas and feedback.

For general discussions about SBGN please join the sbgn-discuss mailing list and bring up your topic there.

For specific questions about this website, workshops or other SBGN resource management topics please send a message to the sbgn-editors mailing list.

SBGN meetings and workshops provide the best environment for learning about the process and for getting involved.

For reporting issues, suggesting enhancements or requesting features please use github.com/sbgn/sbgn/issues.

SBGN Editors

The SBGN editors work towards distilling discussions and requests into coherent specification documents, addressing comments and questions, correcting errata, and generally managing revisions to the SBGN specifications. The editors do not decide what to put in the specifications — they are the voice and the hand of the community. The SBGN editors are elected by the community for 3-year terms as volunteers. There is no limit on the number of terms one can serve as an editor. A serving editor, however, cannot stand for election thereby forcing a gap year between two successive terms.

Adrien Rougny Adrien Rougny, elected for 2022 - 2024, PhD in Computer Science, Independent researcher, Massy, France. Developer of the stonpy tool for converting from SBGN to Neo4j. Developer of the SBGN Bricks Ontology. Leading editor of the SBGN Process Description specification.
Ugur Dogrusoz Ugur Dogrusoz, elected for 2022 - 2024, PhD in Computer Science, Professor at Bilkent University, Ankara, Turkey, and Head of i-Vis Research Lab. PI of the Newt Editor project, an open-source online SBGN editor and visualiser.
Tobias Czauderna Tobias Czauderna, elected for 2023 - 2025, PhD in Bioinformatics, Professor at the University of Applied Sciences Mittweida, Mittweida, Germany; lead developer of the SBGN-ED; involved in the development of LibSBGN, the software library supporting the exchange of SBGN maps.
Augustin Luna Augustin Luna, elected for 2024 - 2026, PhD in Bioinformatics; Research Fellow at the Dana-Farber Cancer Institute, Harvard Medical School, Boston, US.
Rupert Overall Rupert Overall, elected for 2024 - 2026, Senior Researcher at the Humboldt University of Berlin, Germany.

SBGN Acting Editors

Acting Editors are selected among active contributors and are appointed by the elected SBGN Editors. Acting Editors work on particular tasks for intensifying the development of the standard.

Hanna Borlinghaus Hanna Borlinghaus, PhD Student, Research Assistant at the University of Konstanz, Germany. Invited as an Acting Editor in January 2019. A member of the SBGN Team. Contributed to the work on the Process Description specification.
Luiz Ladeira Luiz Ladeira, Postdoctoral Researcher at the GIGA In Silico Medicine, University of Liège, Belgium. Invited as an Acting Editor in October 2023. Contributed to the work on the SBGN Learning materials.

SBGN Delegate at COMBINE

The SBGN standard is part of the COMBINE effort. Each COMBINE standard is represented by a delegate who joins the COMBINE Coordination Board. This delegate can be an editor of the SBGN standard or someone endorsed by the editors. The process by which members of the COMBINE Coordination Board are appointed is described here. The current representative from the SBGN standard:

Falk Schreiber Falk Schreiber, PhD in Computer Science, Professor of Practical Computer Science and Computational Life Sciences in the Department of Computer and Information Science at the University of Konstanz, Germany. PI of the SBGN-ED tool development. Elected SBGN editor for 2008 - 2010 and 2012 - 2014, member of the SBGN Scientific Committee.

Former SBGN Editors

Irina Balaur (Jan 2021 - Dec 2023),
Alexander Mazein (Dec 2015 - Dec 2018, Jan 2021 - Dec 2023),
Emek Demir (Jan 2010 - Dec 2012, Dec 2020 - Dec 2022),
Michael Blinov (Jan 2019 - Dec 2021),
Andreas Dräger (Jan 2018 - Dec 2021),
Adrien Rougny (Jan 2018 - Feb 2021),
Vasundra Touré (Jan 2018 - Feb 2021),
Ugur Dogrusoz (Dec 2016 - Dec 2019),
Augustin Luna (Dec 2014 - Dec 2017),
Robin Haw (Dec 2014 - Dec 2017),
Tobias Czauderna (Jan 2012 - Dec 2015, Dec 2016 - Dec 2017),
Huaiyu Mi (Jan 2009 - Dec 2011, Dec 2013 - Dec 2016),
Alice Villéger (Jan 2011 - Dec 2013),
Nicolas Le Novère (Sep 2008 - Dec 2012, Dec 2015 - Dec 2016),
Stuart Moodie (Sep 2008 - Dec 2011, Sep 2012 - Dec 2015),
Anatoly Sorokin (Sep 2008 - Dec 2009, Jan 2012 - Dec 2014),
Falk Schreiber (Sep 2008 - Dec 2010, Jan 2012 - Dec 2014).

SBGN Scientific Committee

The duties of the SBGN Scientific Committee are to help securing the financial support for SBGN development, to advocate the use of the language in their community, and to check that the development of SBGN is harmonious and democratic. The scientific committee does not have any decision-making power on the content of SBGN, although its advices presumably weight much in the decisions taken by the community.

Principal investigators of grants supporting SBGN development and maintenance are entitled to become members. Other memberships are proposed by the running Scientific Committee and the Editorial Board. Invited members may be pioneers or major players in the field of graphical representation of knowledge, or leading figures in fields that may endorse SBGN. New memberships require unanimity of expressed opinions from current members. The terms of invited members are yearly, renewable without restriction. Renewal must be proposed and seconded by existing members of scientific committee. The current members of the SBGN Scientific Committee:

Kurt Kohn was an invited member between 2009 and 2010. Nicolas Le Novère was a PI and invited member between 2009 and 2015.

SBGN Team

The SBGN Team is created as an initiative of the SBGN editors, following the example of the SBML community. The members of the team develop and maintain the SBGN infrastructure, libraries, and tools. The goal is to make the SBGN effort stronger and ensure its sustainable development. We encourage experts in related standards to participate, so advances in complementary efforts enhance the SBGN development.

Frank Bergmann, PhD in Mathematics / Computational Systems Biology, Member of Scientific Staff at the University of Heidelberg, Germany; a member of the SBML Team and a contributor to several SBML projects; a developer of LibSBGN.

Irina Balaur, PhD in Computational Biology, Researcher at the Luxembourg Centre for Systems Biomedicine, Luxembourg; lead developer of ySBGN, a bidirectional converter between yEd GraphML and SBGN-ML.

Hanna Borlinghaus, PhD Student, Research Assistant at the University of Konstanz, Germany; a member of the SBGN-ED development team.

Emek Demir, PhD in Computer Engineering, Assistant Professor at the Oregon Health & Science University, Portland, USA; a member of the Pathway Commons team and is responsible for the BioPAX development and integration; an editor of the BioPAX standard; interested in the SBGN-BioPAX conversion.

Vasundra Touré, PhD in Bioinformatics, Scientific Coordinator at the Swiss Institute of Bioinformatics; interested in data management and data standardisation in biomedicine and systems biology.

Adrien Rougny, PhD in Computer Science, Postdoctoral Researcher at the National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; the developer of the sbgntikz library for drawing SBGN maps directly in LaTeX; the developer of the SBGN Bricks Ontology; interested in a direct formalization of SBGN maps into qualitative dynamical models.

Alexander Mazein, PhD in Bioinformatics, Researcher at the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg; the coordinator of the SBGN Bricks project.

Andreas Dräger, PhD in Bioinformatics and Systems Biology, Junior Professor at the Institute for Bioinformatics and Medical Informatics (IBMI), Tübingen, Germany; a member of the SBML Team; responsible for the further development of the Krayon4SBGN editor.

Ugur Dogrusoz, PhD in Computer Science, Professor at Bilkent University, Ankara, Turkey, and Head of i-Vis Research Lab; the PI of the Newt Editor project, the development of an open-source online SBGN editor and visualiser.

Augustin Luna, PhD in Bioinformatics; Research Fellow at the Dana-Farber Cancer Institute, Harvard Medical School, Boston, US; interested in the SBGN-BioPAX conversion.

Falk Schreiber, PhD in Computer Science, Professor of Practical Computer Science and Computational Life Sciences in the Department of Computer and Information Science at the University of Konstanz, Germany; PI of the SBGN-ED tool development.

Tobias Czauderna, PhD in Bioinformatics, Research Fellow at the Monash University, Melbourne, Australia; lead developer of the SBGN-ED.

Michael Blinov, PhD in Mathematics, Assistant Professor at UConn School of Medicine, Farmington, US; developer of VCell modelling framework working on the integration of BioPAX and SBGN formats in the modelling; interested in the development of SBGN-compliant rule-based visualisation.

Funda Durupinar, PhD in Computer Engineering, Senior Research Associate at Oregon Health and Science University, Portland, Oregon; the lead developer of the web-based SBGNViz Collaborative Editor; the developer of the PaxToolsAgent, a converter from SBGN to BioPAX.

Rupert Overall, Senior Researcher at the Humboldt University of Berlin, Germany. Invited as an Acting Editor in January 2022. Developer of the Molecular Map of the Aging Neuron. Interested in contributing to preparing SBGN learning materials.

Funding

We are deeply indebted to the many funding agencies and organizations that have supported SBGN over the years.

The development of SBGN during 2005–2008 was mainly supported by a grant from the Japanese New Energy and Industrial Technology Development Organization (NEDO). The principal investigators were Hiroaki Kitano, Akira Funahashi, Nicolas Le Novère and Michael Hucka.

The Okinawa Institute of Science and Technology (OIST), the British Biotechnology and Biological Sciences Research Council (BBSRC) through a Japan Partnering Award, and a US Partnering Award, the European Media Laboratory (EML Research GmbH), the Beckman Institute BNMC at the California Institute of Technology, and US National Science Foundation (NSF) provided additional support for SBGN workshops.

Ownership

No one — not the principal investigators, nor the SBGN Editors, nor the members of the SBGN Scientific Committee, nor the funding agencies or anyone else — owns SBGN; it is a free and open community effort that extends beyond any single group, and we view ourselves only as organizers and fellow developers.