@
MarjaE - calibre version 4 will include a new ebook-viewer that will include annotations and such like, so you might not want to invest too much before seeing what it might provide.
Maybe Kovid will drop a few hints
And maybe the recently added
Entities Manager plugin could be of some use to you. My take on it is this, it provides a set of 'building blocks" (notes, links and associations) with which one can build information networks about authors, books, series, publishers, tags, and user created 'entities'.
Maybe DaltonST will make some comments
Meantime I have another idea, but I need to 'experiment'.
BR