We are thinking quite a bit about pathway tools these days. I got a jolt of input on them from the ICSB meeting recently, too. As I continue to progress through my meeting notes I’ll be checking out more tools and writing about them.
One of the things that seemed new and important (well, to me at least) was the first release of a set of standards for drawing pathway diagrams. During this meeting they announced the release of 1.0 of the SBGN notations (also known as Level 1; more levels are anticipated as this progresses). SBGN is Systems Biology Graphical Notation. You can access the SBGN site here: http://www.sbgn.org/
The idea is that if we can standardize our representations of pathways we can all be sure that the meanings are the same for arrows, and boxes, and so on. For example, if I draw a pathway with an arrow, my arrow means the same thing as your arrow in your pathway diagram.
What the SBGN team says on their homepage:
SBGN defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules defining their use and how diagrams are to be interpreted.
So this is kind of like Gene Ontology for systems and pathway diagrams. Not only is it increasing the clarity of the diagrams, it will guide software development so that software for generating diagrams and analytical tools can work in this framework as well.
There are examples on the web site. Check out the document on the specifications (a big PDF), too–lots of detail on what, how, and why this is important. They want feedback on this. You can also check out the associated SBGN wiki with more details and the SBGN forum for interaction with the team.