The Systems Biology Graphical Notation (SBGN) is a standard

graphical representation Graphic communication as the name suggests is communication using graphic elements. These elements include symbols such as glyphs and icons, images such as drawings and photographs, and can include the passive contributions of substrate, colour ...

intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and

gene regulatory network A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the fun ...

s amongst communities of biochemists, biologists, and theoreticians. The system was created over several years by a community of

biochemist Biochemists are scientists who are trained in biochemistry. They study chemical processes and chemical transformations in living organisms. Biochemists study DNA, proteins and Cell (biology), cell parts. The word "biochemist" is a portmanteau of ...

s, modelers and

computer scientist A computer scientist is a person who is trained in the academic study of computer science. Computer scientists typically work on the theoretical side of computation, as opposed to the hardware side on which computer engineers mainly focus (al ...

s. SBGN is made up of three orthogonal languages for representing different views of biological systems: ''Process Descriptions'', ''Entity Relationships'' and ''Activity Flows''. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules regarding the construction and interpretation of maps. Using these three notations, a life scientist can represent in an unambiguous way networks of interactions (for example

biochemical Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology an ...

interactions). These notations make use of an idea and symbols similar to that used by electrical and other engineers and known as the

block diagram A block diagram is a diagram of a system in which the principal parts or functions are represented by blocks connected by lines that show the relationships of the blocks.

. The simplicity of SBGN syntax and semantics makes SBGN maps suitable for use at the high school level. Some software support for SBGN is already available, mostly for the Process Description language. SBGN visualizations can be exchanged with the XML-based file format SBGN-ML.

SBGN Process Description language

The SBGN Process Description (PD) language shows the temporal courses of biochemical interactions in a network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram.Moodie SL, Le Novère N, Demir E, Mi H & Villéger A. Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings (2011)

SBGN Entity Relationship language

The SBGN Entity Relationship (ER) language allows to see all the relationships in which a given entity participates, regardless of the temporal aspects. Relationships can be seen as rules describing the influences of entities nodes on other relationships.Le Novère N, Demir E, Mi H, Moodie S & Villéger A. Systems Biology Graphical Notation: Entity Relationship language Level 1
Nature Precedings (2010)

SBGN Activity Flow language

The SBGN Activity Flow (AF) language depicts the flow of information between biochemical entities in a network. It omits information about the state transitions of entities and is particularly convenient for representing the effects of perturbations, whether genetic or environmental in nature.Mi H, Schreiber F, Le Novère N, Moodie S, Sorokin A. Systems Biology Graphical Notation: Activity Flow language Level 1
Nature Precedings (2009)

History

Work on defining a set of symbols to describe interactions and relationships of molecules was pioneered by Kurt Kohn at the

National Cancer Institute The National Cancer Institute (NCI) coordinates the United States National Cancer Program and is part of the National Institutes of Health (NIH), which is one of eleven agencies that are part of the U.S. Department of Health and Human Services. ...

with his

Molecular Interaction Maps Molecular Interaction Maps, also known as MIMs, is a graphic notation to depict cellular and molecular interactions. It was created by Kurt W. Kohn in 1999.Kohn KW. Molecular interaction map of the mammalian cell cycle control and DNA repair system ...

(MIM).Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology
Mol Biol Cell (2006)
The development of SBGN was initiated by

Hiroaki Kitano is a Japanese scientist. He is the head of th Systems Biology Institute(SBI); President and CEO of Sony Computer Science Laboratories; a Group Director of the Laboratory for Disease Systems Modeling at and RIKEN Center for Integrative Medical ...

, supported by a funding from the Japanese

New Energy and Industrial Technology Development Organization The , or NEDO, is Japan's largest public management organization promoting research and development as well as deployment of industrial, energy and environmental technologies. In 2003, NEDO was reorganized as an Independent Administrative Institu ...

. Th
meeting that initiated
development of the Systems Biology Graphical Notation took place on February 11–12, 2006, at the National Institute of Advanced Industrial Science and Technology (AIST), in Tokyo, Japan. The first specification of SBGN Process Description language – then called Process Diagrams – was released on August 23, 2008 (Level 1 Version 1).Le Novère N, Moodie S, Sorokin A, Hucka M, Schreiber F, Demir E, Mi H, Matsuoka Y, Wegner K, Kitano H. Systems Biology Graphical Notation: Process Diagram Level 1
Nature Precedings (2008) doi:10101/npre.2008.2320.1
/ref> Corrections of the document were released on September 1, 2009 (Level 1 Version 1.1),Moodie S, Le Novère N, Sorokin A, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings (2009)
October 3, 2010 (Level 1 Version 1.2)Moodie SL, Le Novère N, Demir E, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings (2010) doi:10101/npre.2010.3721.2
/ref> and February 14, 2011 (Level 1 Version 1.3). The first specification of SBGN Entity relationship language was released on September 1, 2009 (Level 1 Version 1).Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1
Nature Precedings (2009)
Corrections of the document were released on October 6, 2010 (Level 1 Version 1.1)Le Novère N, Moodie S, Demir E, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1
Nature Precedings (2010)
and April 14, 2011 (Level 1 Version 1.2). The first specification of SBGN Activity Flow language was released on September 1, 2009.

Editors

SBGN editors work in developing coherent specification documents. Below is a list of former SBGN editors and dates active: * Ugur Dogrusoz (Jan 2022 - Dec 2024) * Adrien Rougn (Jan 2022 - Dec 2024) * Alexander Mazein (Jan 2021 - Dec 2023) * Irina Balaur (Jan 2021 - Dec 2023) * Emek Demir (Jan 2020 - Dec 2022) *

Andreas Dräger Andreas Dräger (; born 20 September 1980) is a German bioinformatician who leads the research group for Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens at the University of Tübingen. Education In high sch ...

(Jan 2018 - Dec 2021) *

Falk Schreiber Falk may refer to: * Falk (name), including origin and list of people with this name * Falk, California, a ghost town * Falk Township, Minnesota * Postal abbreviation of Falkirk, an area of Scotland See also *Falx (disambiguation) *Faulk (disamb ...

(Sep 2008 - Dec 2010, Jan 2012 - Dec 2014) * Anatoly Sorokin (Sep 2008 - Dec 2009, Jan 2012 - Dec 2014) * Stuart Moodie (Sep 2008 - Dec 2011, Sep 2012 - Dec 2015) * Nicolas Le Novère (Sep 2008 - Dec 2012, Dec 2015 - Dec 2016) * Emek Demir (Jan 2010 - Dec 2012) * Alice Villéger (Jan 2011 - Dec 2013) * Huaiyu Mi (Jan 2009 - Dec 2011, Dec 2013 - Dec 2016) * Tobias Czauderna (Jan 2012 - Dec 2015, Dec 2016 - Dec 2017) * Robin Haw (Dec 2014 - Dec 2017) *

Augustin Luna Augustin may refer to: * Augustin (name), male name, variant of Augustine * Augustin (typography), English or 14-point type * Augustin, Brașov, a commune in Brașov County, Romania * Dacian fortress of Augustin, ruined Dacian fortified town in ...

(Dec 2014 - Dec 2017) * Alexander Mazein (Dec 2015 - Dec 2018) * Ugur Dogrusoz (Dec 2016 - Dec 2019) * Vasundra Touré (Jan 2018 - Feb 2021) * Adrien Rougny (Jan 2018 - Feb 2021)

External links

* http://sbgn.org/

References

{{COMBINE Systems biology Notation