Is there a commonly used markup language for graphs (the topological kind). I would expect XMLelements such as Node and Edge and attributes showing directionality and labels 

UPDATE:
So far there is a choice of 2, GraphML and DotML. GraphML hasn't changed since 2007 but maybe it doesn't need to! SO readers may wish to know what toolsets each have - I am encouraged that Gephi uses GrahML, and obviously DotML has the GraphViz and other toolsets. (I shall be writing a limited toolkit in Java for whichever language I choose)

UPDATE: 
I am personally going with DotML. I need the language for modelling (e.g. adding labels, weights, etc. to nodes and edges so will need my own additional namespace). The attraction of DotML is that it seems to be active, and that graphViz can make use of the output. YMMV