I’ve been (slowly) pecking away at trying to own all of this type of data on my own website. It sounds like what you’re hoping for is a cross between Derek Sifford’s Academic Blogger’s Toolkit which has a pretty slick WordPress interface for looking up and importing references and David Shanske’s Post Kinds Plugin which allows one to create specific post types like bookmarks, reads, notes, highlights, annotations, etc.
I think if Academic Blogger’s Toolkit could create an internal database within WordPress and an interface to allow you to easily import/export it as well as use it within your own instance, that might be the simplest solution to have ownership over all of one’s reference data. The Post Kinds plugin would give you the rest including the ability to hide your posts as private just to you or others granted access on your site.
Like Greg McVerry, Ian O’Byrne, Aaron Davis, and others I use my own site like a commonplace book and store bookmarks of things I’d like to read as well as things that I have read, usually along with notes, highlights, annotations, and other marginalia that I think would be of use.
Perhaps by adding one or two extensions, WordPress could be the perfect platform for doing this type of work without reliance on external sites?