I keep an eye on personal knowledge management (PKM) applications because of their close relationship to personal learning environments. This article compares two market leaders, Obsidian and Roam.Each of them has a graph view (pictured) but in my experience it's difficult to really use a graph view to do things; rather, to me at least, the grapg is the thing behind the scenes that keeps track of relationships to the application can do just the right thing at the right time
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