So I have an SBGN-ML file, what’s next?

The Systems Biology Graphical Notation (SBGN) is a system for drawing pathways in a very precise and standardized way. But the problem is that the software support is spotty at best. The LibSBGN project is here to help improve that situation (For a bit of history, see here and here). As part of this project, we created a file format for SBGN files, named SBGN Markup Language or SBGN-ML.

Let me break that alphabet soup down for you:

  1. SBGN: the graphics
  2. LibSBGN: the software
  3. SBGN-ML: the file format

Suppose you manage to procure a SBGN-ML file. You may then reasonably ask what you can do with it. Until fairly recently, the only answer that we could give to non-programmers was “not much”. That is quickly changing however. I’ll present three things you can do with an SBGN-ML file right now.

1. Open it in PathVisio

Using the following webstart link, you can open PathVisio with the SBGN-plug-in pre-installed. (More information about the state of this plug-in, see the help page). Then go to File->Import… and select SBGN-ML from the file type drop-down.

2. Convert them into an image from the Command-Line

If you want to convert a bunch of SBGN-ML files to images, it’s easier to do it from the command-line. For this purpose I created a little script. First download the sbgn-to-png tarball. Unzip it, and run it from the command line using “sh “.

3. Open it in SBGN-ED

The SBGN-ED tool is an alternative to PathVisio for editting pathway diagrams. SBGN-ED has won the annual SBGN competition in the category “Best software support” twice in a row.

When comparing PathVisio and SBGN-ED, the latter is probably a bit better when it comes to editing Process Description diagrams, whereas PathVisio deals better with Entity Relationship diagrams. The only caveat is that at this time of writing, SBGN-ED only supports an older version of SBGN-ML. For this reason, files generated by SBGN-ED can be read by PathVisio, but not the other way around. An update should arrive very soon though.

Tags: , ,

Comments are closed.