Systems Biology Graphical Notation
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The Systems Biology Graphical Notation (SBGN) is a standard graphical representation crafted over several years by a community of biochemists, modelers and computer scientists[1].
Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms, a life scientist can represent in an unambiguous way networks of biochemical interactions. The sets of symbols used is limited, and the grammars quite simple, to allow its usage in textbooks and its teaching directly in high schools.
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[1][2].
The SBGN Entity Relationship (ER) language allows you 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[3].
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[4].
Some software support for SBGN is already available, mostly for the Process Description language.
Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory network.
History
The development of SBGN was initiated by Hiroaki Kitano, supported by a funding from the japanese New Energy and Industrial Technology Development Organization.
The first specification of SBGN Process Description language - then called Process Diagrams - was released on August 23rd 2008 (Level 1 Version 1)[1]. A correction of the document was released on September 1st 2009 (Level 1 Version 1.1)[2].
The first specification of SBGN Entity relationship language was released on September 1st 2009[3].
The first specification of SBGN Activity Flow language was released on September 1st 2009[4].
External links
References
- ^ a b c Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nature Biotechnology (2009), 27(8): 735-741. Cite error: The named reference "Lenov2008" was defined multiple times with different content (see the help page).
- ^ a b Moodie S, Le Novère N, Sorokin A, Mi H, Schreiber F. Systems Biology Graphical Notation: Process Description language Level 1. Nature Precedings (2009) doi:10.1038/npre.2009.3721.1
- ^ a b Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H. Systems Biology Graphical Notation: Entity Relationship language Level 1. Nature Precedings (2009) doi:10.1038/npre.2009.3719.1
- ^ a b Mi H, Schreiber F, Le Novère N, Moodie S, Sorokin A. Systems Biology Graphical Notation: Activity Flow language Level 1. [http://precedings.nature.com/documents/3724/version/1 Nature Precedings (2009) doi:10.1038/npre.2009.3724.1