Looking for a better workflow re: epub files (annotate and then export annotations)

Maybe someone in this forum can help me with reading > annotating > note taking epub files.

My regular workflow with pdfs is to annotate them (highlights app, PDF expert or DT) and then export / summarise the highlights or notes to DT where I reorganize them joining my ideas and research notes (aka reading notes).

The other major format for books nowadays is epub. Alas, unlike pdfs, it has been very difficult to have a good workflow to annotate > process my notes.

In the iPad I’ve been using MapleRead: a great reading app, that allows highlights and notes, but only exports them directly in csv, which is a pain to use to prepare my reading notes; or via a cloud service (in HTML format), which takes extra time.

In the Mac it’s even worse, since no epub reader (kobo, books…) has capable exporting features. Calibre ebook-viewer is better, but still not that great. (Often I prefer to convert epub to pdf and then annotate…)

Is anyone annotating > processing notes in epub files? Any ideas on how to better do this?

Well, there is no standard for annotating ePUBs. So every reader does what its developers deemed nice or feasible or useful or whatever.


Yes, that’s what we’d suggest as well.

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Yeah. And that is such a pain! For such an important format, the lack of annotation features in epub (specially export) is quite disappointing. I wonder how much that has to do with DRM and the fear of pirated ebook…


That, and probably not a recognised/implemented standard (other than based on HTML), along with attempts at vendor lockin.


Try the app yomu. Exports annotations directly to markdown. For Mac/ios/iados.


Marginnote https://www.marginnote.com/

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Here’s my solution (this was only possible not too long ago).

  1. Get you DRM-free ePub.

  2. Upload to Kindle. After much experimentation I found that the best way is to use the “Send to Kindle” website. Search for “send to kindle” in your favourite search engine. Most, but not all, epubs make the grade and can be uploaded.

  3. Enjoy the reading experience and synchronisation across all your devices.

  4. To export your annotations: in any Kindle app (they all have the same interface on whatever platform or device, thanks to the switch-over to React native) show your annotations with the following icon.


Then click the share icon.

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  1. At this point you will find the only limitation - that you can only email your annotations. I don’t find that adds any more friction than downloading to a folder because I have my email app running constantly in the background, anyway.

If you use the latest version of the Kindle app, you can even choose how the citations will be formatted, or sans citations if you prefer.

The annotations will be exported in HTML, but that’s not a problem for us Devonthink3 users, right?

In addition, if the book is DRM free, you can export as much highlighted text as you want, in contrast to a DRM protected book.

  1. Find the email. You don’t need to download the attachment, Just drag the HTML attachment directly into Devonthink3.

  2. From there, convert to any other format to your heart’s content, use rules process the file etc etc.

Before Amazon opened Kindle to side-loaded (or in this case up-loaded) epubs, I had the same problem as you, cursing Apple for trapping annotations made in Books in a SQLite database with no easy way to export.

Finally, just another tip, or rather this is something else I do: I store all my epub books (and PDFs as well) in Devonthink3. That way, I can use DT to search through the content of all of my epubs. To view the content of epubs you need to make sure you are in “Source” mode.

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Alas I don’t have a Kindle. I use iPad (and, once in a blue moon, a Kobo).

Yomu seems to work quite well for what I want. Thanks for the idea. :slight_smile:

You don’t need a Kindle. Just download the Kindle app on your iPad (and iPhone) and Mac. Then all you need is an Amazon account to link them all!

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I’ll try this. Thanks for the idea. :slight_smile: