keep book, ebooks or any publication reference and links

It would be great to be able to save book references and manage collections in order to :

Access to a list of ebooks and other electronic publications to read them.
Create, share, search for books, ebooks or publications (online or not) references,
import a bibliography in a document,
save online articles to disk.
Take notes on the publication, print them, share them.

Integration and problems

Integrating documents such as PDF into the application creates a risk of conflict between searching books as a leisure and managing a huge document library.
Dealing with articles/ebooks that are accessible on the computer and real books or non accessible books might conflict.

We might make a difference between create a bookmark to go often to an adress (access to webmail quickly for example) and bookmarks used to remind a specific page (hostel page, online article etc.)
Users could in a single click save the content of the page, URL and metadata of the webpage (if an article, authors, newspaper etc.)

These references might be taken from epiphany

create an app that deals with ebooks only or ebooks and other publication documents (saved on the disk).
create another app aimed specifically to managing bibliography, research project etc. The problem of what to import in it still exist : what is a publication (which documents to import from disk to such an app ?) ? How to get metadata without the users having to fill it ?
integrate to epiphany a system to archive webpages and metadata for publications

Or:

Create a single app that include references to real books, electronic publications, available or not.