Some design comments:
The concepts in a MindRaider notebook are organized in a hierarchical way, clearly visible in the notebook panel. In contrast, the graph navigator - as it's implemented now - is non-directional, with the current concept in the middle, and the related concepts "spread out" 360 degrees around. This inconsistency might account for your uneasyness with graph navigation (which I sense from your plans for vodyanoi)?.
It does not have to be that way, though: Quite a while ago, Alex Shapiro had created an alpha version of a touchgraph brain browser, which takes into account the hierarchical nature of the way thoughts are organized in thebrain. And in the graph, the "lower" levels did not "spread out" 360 degrees around the particular thought/concept, but only 180 degrees or so. Thus the network/graph became directed, with some slack. See http://www.touchgraph.com/TG_TheBrain_DemoBrain.JPG . A good blend between hierarchy and network. The source code for TGBrainBrowser was never released, potential patent/design issues. Thus I don't know how this was done. But you might be able to find out ;-)
Off-topic? No. Borderline, may be:
A great paper - not about MindRaider but about "The Pyramid and the Net:
The Postmodern Adventure in Biblical Studies".
You may ignore the content (biblical studies), but the rest is exactly about that aspect here: hierarchy vs. network, how both "shapes" complement each other, and how this is related to cognition:
I think that being able to create networks should be the regular - think on a way to create an RDF based toc file for Websites witch describes and summaries all of the link functionality of <link rel="..." href="..." /> elements.
I don't know about the RDF syntax (so excuse the pseudocode) but it should be able to provide somthing like:
Yes, exactly - and in fact it is already there (but not documented and not easily usable).
Just try to click right mouse button over the node in Graph explorer and you will be allowed to create any RDF triplet.
Note that this features is being developed so it shouldn't be used (such changes are not saved, notebooks are not automatically changed, etc.) so you may experiment, but I suggest you to do it in RDF Model mode or in some "Trainer" concept ;-)
Definitely there will be this feature in the MR - many users have this requirement :-)
Thanks for the feedback!
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