After months of work, last week we finally released the first version of LibSBGN.
So what is LibSBGN? The Systems Biology Graphical Notation (SBGN), is a standard for drawing pathways. It prescribes exactly how to draw a biochemical reaction, how one can display the effect of heat on protein degradation, or how you should present the formation of a protein complex. It’s unambiguous: no matter how complex the drawing gets, it can be interpreted in only one way. SBGN is the result of many discussions, arguments and debates, over the course of several years and it’s therefore really well thought out.
Good software support is essential to make SBGN succeed as a standard. LibSBGN was created in an attempt to encourage uptake. As the name implies, LibSBGN is a software library that should make it easy to incorporate SBGN in pathway tools.
LibSBGN is only a software component, it’s not a ready to use end-product by itself. So this announcement is probably only interesting to bioinformatics developers. Nevertheless, I hope that it will soon lead to an increased uptake of SBGN in pathway tools, which should benefit end-users of those tools as well.
LibSBGN is already supported by a few applications, including of course PathVisio. To make sure that it works exactly the same in each tool, we’ve created a comparison gallery, containing several test-cases rendered by each tool. All the diagrams should look exactly the same for each tool. This comparison page has proven tremendously useful to check for bugs and misunderstandings.
This is only the first release, there is still a lot to do. This first release only supports a part of SBGN called process description (PD). The coming months will see lots of work on the remaining parts of SBGN, entity relationships (ER), and activity flow (AF). And after that we’ve planned more features, such as validation rules and file format conversion.
This is the first tangible result from something that was set in motion at a meeting in Wittenberg. LibSBGN community: thanks for your hard work and congratulations on this first milestone.
