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A Community Effort Leads the Way to Standard Data Specs

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It looks like a three-year effort to help systems biology investigators better record and share experimental data is beginning to show some promise. The Systems Biology Graphical Notation project, a multi-national effort headed up by researchers at the European Bioinformatics Institute, has recently released the first of three specifications for systems biologists to depict biochemical and cellular reactions. Those behind the SBGN project are aiming to make theirs a universally accepted way of graphically representing this data so that communication between researchers is no longer a roadblock.

"Graphic annotation has been standardized in physics and engineering, but in biochemistry, there was never an attempt to standardize annotation for everyone," says Nicolas Le Novère, a group leader at EBI and one of five current editors of the SBGN project. "When you have those large maps of networks, if you know what's in there, you can understand it."

The SBGN group marks the first time there has been an agreed-upon convention for descriptive and compressive graphical language so that diagrams can be exchanged seamlessly between researchers. The SBGN standard will include three components: a process diagram notation system, which will show the temporal courses of biochemical interactions in a particular network; an entity relationship notation; and an activity flow notation, which offers a standardized representation of biochemical relationships and signal flow in a given entity. "At the moment, we've only released the process diagram because it is the language that is the easiest to develop software support for," says Le Novère. "For us, it was really important to develop software support and deliver something for the end user."

The contributors say the real payoff will come when researchers are as familiar with their notation as electronics engineers are with circuit schematics. If researchers can save time and effort on familiarizing themselves with different notations, they can spend more time thinking about the biology that's being depicted.

Le Novère says the real challenge is coming up with a solution that caters to everyone. "We started to discuss this over three ago and it took a long time to even release the first level because … you have to discuss with as many people as possible so they can break your work so you get it better."

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