The Magpie site has a flash demo of their system for semantic markup. My main interest is in the user interaction: rather than a disembodied index, information is presented inside the text. In my professional life, we've been doing this with name markup for nearly 10 years. We've always found the UI gets a lot more complicated when you start to include relationships. But i like their notion of a right-click menu that brings up a set of relationships that an entity participates in, and that enable you to browse to a new point (though what happens when you click that relationship link is the key question).

This may be a good alternative to this interface concept for the New Testament Names data.