The Systems Biology Graphical Notation (SBGN) is a standard graphical representation crafted over several years by a community of biochemist

Biochemist

Biochemists are scientists who are trained in biochemistry. Typical biochemists study chemical processes and chemical transformations in living organisms. The prefix of "bio" in "biochemist" can be understood as a fusion of "biological chemist."-Role:...

s, modelers and computer scientist

Computer scientist

A computer scientist is a scientist who has acquired knowledge of computer science, the study of the theoretical foundations of information and computation and their application in computer systems....

s.

SBGN languages are intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory network

Gene regulatory network

A gene regulatory network or genetic regulatory network is a collection of DNA segments in a cell whichinteract with each other indirectly and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA.In general, each mRNA molecule goes...

s amongst communities of biochemists, biologists, and theoreticians.
The simplicity of SBGN syntax and semantics makes SBGN maps suitable for use at the high school level.

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 interactions). These notations make use of an idea and symbols not that far removed from that used by electrical and other engineers and known as the block diagram

Block diagram

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....

Some software support for SBGN is already available, mostly for the Process Description language.

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

Interactome

Interactome is defined as the whole set of molecular interactions in cells. It is usually displayed as a directed graph. Molecular interactions can occur between molecules belonging to different biochemical families and also within a given family...

 taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram.

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.

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.

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

National Cancer Institute

The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...

 with his Molecular Interaction Maps

Molecular Interaction Maps

Molecular Interaction Maps, also known as MIMs, is a graphic notation to depict cellular and molecular interactions created by Kurt W. Kohn in 1999 . The MIM convention is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that...

 (MIM). The development of SBGN was initiated by Hiroaki Kitano

Hiroaki Kitano

is a Japanese scientist who currently works for Sony Computer Science Laboratories and is best known for developing AIBO, and the robotic world cup tournament known as Robocup. He graduated from International Christian University in 1984 and received a Ph.D. in engineering from Kyoto University in...

, supported by a funding from the Japanese New Energy and Industrial Technology Development Organization

New Energy and Industrial Technology Development Organization

The New Energy and Industrial Technology Development Organization , also known as 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...

. The meeting that kicked off the 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). Corrections of the document were released on September 1, 2009 (Level 1 Version 1.1), October 3, 2010 (Level 1 Version 1.2) 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). Corrections of the document were released on October 6, 2010 (Level 1 Version 1.1) and April 14, 2011 (Level 1 Version 1.2).

The first specification of SBGN Activity Flow language was released on September 1, 2009.