Research News
Developing A Symbolic Language For Systems Biology
Not long ago, our understanding of the genetic and biochemical workings of a cell were simple enough that they could be represented in easy-to-comprehend two dimensional flow diagrams. Today, however, it is clear that this two-dimensional view cannot do justice to the complexity of the biochemistry and genetics that operate in a cell, and that biologists need a better graphical notation for a systems biology approach to life.
Now, taking a page from computer scientists, who have developed a rich graphical language for representing ever-more-complex computer circuitry, an international team of nearly 40 biochemists, modelers and computer scientists has created the Systems Biology Graphical Notation (SBGN) that it believes represents a good starting point for a visual language for biologists. This work appears in the journal Nature Biotechnology.
The SBGN project, which began in 2005, aims to create a systematic and unambiguous symbolic language for use in molecular and systems biology. Rather than try to create a complete language that covers all biological systems, the investigators decided to create a framework that could work today and yet grow to accommodate future advances in understanding of how biological systems are organized. One of the bedrock rules of SBGN is that it specifies the connections, nodes and edges that define a given system without defining the precise layout of the graphs, the relative position of symbols on the graph, or on the use of colors, shading and other graphical elements prone to misreading and misinterpretation.
SBGN also determined that representing all the possible components, reactions and interactions on a single diagram was futile. As a result, the project’s investigators defined three complementary types of diagrams that can each represent specific aspects of a given system. The process diagram, which resembles classical biochemical pathway drawings in textbooks, portrays the time-dependent qualities of the molecular transformations that occur in cells. The entity relationship diagram emphasizes the influences that the entities in these transformations have on each other, rather than on the transformations themselves. This diagram provides an easy-to-grasp view of all the possible interactions and influences affecting a given cellular entity. Finally, the activity flow diagram presents the various stimulatory and inhibitory influences that impact the processes represented in the other two diagrams.
SBGN has created a Web portal for anyone interested in learning more about the project or participating in future language development. The portal is accessible at http://sbgn.org.
This work, which was supported in part by the National Cancer Institute, is detailed in a paper titled, “The Systems Biology Graphical Notation.” Investigators from 31 institutions contributed to the paper. An abstract of this paper is available at the journal’s Web site.
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