Backlinks/Deep links for ebook highlights

Dear all,

Apologies in advance for this rather extensive post. I have just pondered over this question for some time now, but I’m still not satisfied with the option I figured so far. I basically want to extract the annotations from ebooks I read to my note-taking app with a backlink to the specific page inside the respective ebook.

I figured this process for pdfs, where there are solid options with Zotero & Zotfile as well as the Highlights pdf app. With the Highlights app, for instance, the result looks like this:

Above all, as I have shown, this imaginary was the outcome of a gradual, long-term, bottom-up formation, always in need of rehearsal and (re)stabi- lization [Page 128] (highlights://Jasanoff_Kim_2015_Dreamscapes%20of%20Modernity%20-%20Sociotechnical%20Imaginaries%20and%20the%20Fabrication%20of%20Power#page=128))

However, for ebooks I only found to options:

  1. Calibre’s ebook reader offers precisely this for macOS. The reader (as the app) itself is pretty amazing and highly customisable. However, there are two downsides.

    1.1 (minor): There is no shortcut or let alone automation option. So, for every annotation I have to use the UI and click around and then manually transfer the annotations with copy&paste into my note-taking app.

    1.2. (major): I could kind of live with this minor downside. However, I normally read ebooks with the iPad and there is literally only one reader called Marvin that integrates with Calibre. Unfortunately, Marvin itself wasn’t updated in three years or so and the integration with Calibre could break at any point. Which is too risky as to build a reliable workflow on it.

    1.2.1. Apple’s Books app isn’t an alternative. As you may know, the ebooks there reside within a specific folder inside the cloud in an archive format- so not as an epub etc… Accordingly, Calibre’s ebook viewer can’t read the ebooks or annotations from the Apple Books directory.

    1.2.2. Even if it could read the ebooks, it seems annotations are never stored inside the ebook itself. So, apparently, the only solution would be an ebook app that works on the Mac and the iPad. Which brings me to the second option.

  2. I haven’t checked this option myself. But, apparently, the amazing Readwise service offers backlinks for annotations from Kindle books. One only need the Kindle app installed to make use of them. I could, thus, read all my ebooks with the Kindle app on my iPad, sync the annotations to Readwise and from there to my note-taking app, and then open these links with the Kindle app on my Mac.

However, also there are two downsides here.

2.1. I don’t want to support Amazon in anyway because of their attitude towards taxes and how they treat their workers.

2.2. Most of my ebooks are epubs and will be probably also be in the future (if I buy them directly from the publisher.) Sending them each time to the my Kindle/Amazon email seems like waste of time.

The only option I haven’t checked so far would be Devonthink. I think DDTG can handle epubs, but I don’t know how nice the user experience is (I think it is superb for Apple Books) and if DT offers backlinks for epub annotations (as they do for pdfs).

For now, I will probably read my ebooks with Apple’s Books app and then manually process them on my Mac with Calibre. Still, I can’t believe that it is 2022 and there are still no other options to integrate ebook annotations in an efficient workflow than relying on Amazon. Maybe I’m completely wrong though and there are some other options?


Check out MarginNote. MarginNote imports both PDF and ePUB document. There are numerous methods for marking up and taking notes, and each note can have a marginnote://... link.

For example, this page, highlight, and accompanying note that I have in MarginNote from Ahren’s “How to Take Smart Notes” ePUB.

The link to this particular note is marginnote3app://note/b3ddf17f-5ce5-6084-3362-3565098b62c0

Any PDF or ePUB that I markup and take notes on in detail is usually done in MarginNote. I’ve tried many alternatives; this is the best

Available to macOS and iPadOS (and iOS, but the form factor there is too small).


If Libby is available where you’re located, Readwise now works with it:


Thanks for the hint! Will give MN a try then :slightly_smiling_face:
Thanks also @acavender!

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