It would be great if there was a way to link entries of the bibliography together (e.g. links as "is a generalization of", "has experimental facts about", "contains a counter-example of", etc.).
Ideally, links should be user defined, and a graphical representation of the links between the entries would be a must.
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This is exactly what I have looking for. Formally, I have been trying to find an application allowing we to record the reason why I followed a reference. A bonus would be to see this graphically.
Visually linked references are offered by the JabRef PRRV Plugin: http://sourceforge.net/projects/jabrefprrvp/