Systems Biology Graphical Notation
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]
SBGN is made up of three orthogonal languages, the Process Descriptions, the Entity Relationships and the Activity Flows, representing different visions of biological systems. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules how maps are to be interpreted. Using these three idioms, a life scientist can represent in an unambiguous way networks of interactions, for instance (but mot limited to) biochemical. 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.
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.[2]
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.[3]
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.[4]
Some software support for SBGN is already available, mostly for the Process Description language.[5] Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages intends to foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory network.
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 with his Molecular Interaction Maps (MIM) [6]. 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).[7] Corrections of the document were released on September 1st 2009 (Level 1 Version 1.1)[8] and October 6th 2010 (Level 1 Version 1.2). [2]
The first specification of SBGN Entity relationship language was released on September 1st 2009.[3] and the first specification of SBGN Activity Flow language was also released on September 1st 2009.[4]
External links
References
- ^ Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A; et al. (2009). "The Systems Biology Graphical Notation". Nat Biotechnol. 27 (8): 735–41. doi:10.1038/nbt.1558. PMID 19668183.
{{cite journal}}: Explicit use of et al. in:|author=(help)CS1 maint: multiple names: authors list (link) - ^ a b 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
- ^ 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. Nature Precedings (2009) doi:10.1038/npre.2009.3724.1
- ^ "Community#SBGN_Software". sbgn.org. Retrieved 2009-11-30.
- ^ Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2006) doi:10.1091/mbc.E05-09-0824
- ^ 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
- ^ 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