Shown above is a summary of the physiology of a neuro-muscular junction in a newly introduced visual language called Systems Biology Graphical Notation (SBGN). Developed to standardize and simplify a knowledge database in an exploding field of Systems Biology, the language is touted to represent “networks of biochemical interactions in a standard, unambiguous way” in order to “foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.”
Caltech has released the following statement about SBGN:
SBGN will make it easier for biologists to understand each other’s models and share network diagrams more easily, which, Hucka says, has never been more important than in today’s era of high-throughput technologies and large-scale network reconstruction efforts. [Michael Hucka is a senior research fellow and codirector of the Biological Network Modeling Center at Caltech’s Beckman Institute –ed.] A standard graphical notation will help researchers share this mass of data more efficiently and accurately, which will benefit systems biologists working on a variety of biochemical processes, including gene regulation, metabolism, and cellular signaling.
“Finally, and perhaps most excitingly,” adds Hucka, “I believe that, just as happened with the engineering fields, SBGN will act as an enabler for the emergence of new industries devoted to the creation of software tools for working with SBGN, as well as its teaching and publication.”
Previous graphical notations in biology have tended to be ambiguous, used in different ways by different researchers, and only suited to specific needs–for example, to represent metabolic networks or signaling pathways. Past efforts to create a more rigid notation failed to become accepted as a standard by the community. Hucka and his collaborators believe that SBGN should be more successful because it represents a more concerted effort to establish a standard by engaging many biologists, modelers, and software-tool developers. In fact, many of those involved in the SBGN effort are the same pioneers who proposed previous notations, demonstrating the degree to which they endorse SBGN as a new standard.
To ensure that this new visual language does not become too vast and complicated, the researchers decided to define three separate types of diagram, which describe molecular process, relationships between entities, and links among biochemical activities. These different types of diagrams complement each other by representing different “views” of the same information, presented in different ways for different purposes, but reusing most of the same graphical symbols. This approach reduces the complexity of any one type of diagram while broadening the range of what can be expressed about a given biological system.
To learn more about SBGN, follow these links:
Abstract in Nature Biotechnology: The Systems Biology Graphical Notation Nature Biotechnology 27, 735 – 741 (2009)
Press release: Caltech Scientists Help Launch the First Standard Graphical Notation for Biology…
Flashback: BioModels: a Computational Systems Biology Database