iBooks, Annotation, ePub and iCloud syncing

A journey through the exciting world of taking notes on novels, textbooks and such.

I’ve been looking for the best way to annotate digital reference sources I get for a while. Lots of technical manuals for Avid, Boris, FCP, my air conditioner, etc, are available in PDF format, and with the mountain of applications available to annotate PDFs on the iPad, it’s easy to make a folder on Dropbox and simply sync all my PDFs. The files are readable by a variety of apps, and I have ready access to them from anywhere I’ve got an internet connection. I’ve been using this system for a couple of years and it works well.

But there are some kinds of reference works that aren’t great as PDFs – basically, anything longer, without a lot of pictures. For instance, for my current show, my copy of One Minute to Midnight. If digital files had spines, this one would be cracked, and if it were a paperback, it would have more pages with dog ears than without. There would also be post-it notes all over it.

In trying to duplicate that mess in a digital model, I want a system that does the following:

  1. Allows me to read my documents on at least my iPhone and my iPad.
  2. Enables me to make annotations on ANY device I can read on.
  3. SYNC annotations across those devices.
  4. Not lock me in to that format forever. I need to be able to get my notes out by exporting, or emailing them to myself.

If you buy a book from Amazon, things work pretty well – you can highlight and make notes on your desktop, iPad, iPhone and Kindle. Which is great…except I haven’t found a way to get my notes out of Amazon’s system. Admittedly, if I wrote in the margins of a book, I can’t get those notes automatically into a word processor, but a digital book shouldn’t be subject to the limitations of a physical one.

Since I wasn’t happy with the Amazon walled garden, I started investigating iBooks and the ePub format. iBooks can open PDFs and ePub files, in addition to books you purchase from Apple’s iBook store. Books purchased from the iBook store can automatically get pushed to all your devices, the same way that Apps and Music do, if you’ve turned that option on. Highlighting is very easy – easier than the Kindle apps – with five color choices as well as underlining, and it’s easy to make notes as well. And most importantly, you can then email them to yourself. These emails don’t contain highlights, just notes; and they don’t contain info about where the note was either, which would be nice. But that’s easily worked around by simply copying a couple of sentences from the main text into the note. So with very little effort, there’s a decent system here for reacting to a text, and then collecting those reactions & notes for later.

So iBooks is meeting three of my four conditions. But if you open up an ePub into iBooks that doesn’t come from Apple’s store, it does not automatically become ubiquitous. So, it appears at first that the syncing doesn’t work the way I wanted it to.

In fact, that’s not correct. Here’s what actually happens: if you take a DRM free ePub you’ve acquired and open it into iBooks on an iPad, you can read it, and use the full range of iBooks tools to annotate the file. The file does NOT automatically appear on your iPhone, regardless of what settings you’ve enabled. But, if you take the extra step of opening that same file up in iBooks on an iPhone tied to the same iCloud account, the annotations, notes and bookmarks do in fact sync between devices. Changes seem to only get pushed up to the cloud when you close the file by tapping the library icon, but at that point new notes, highlights and bookmarks get saved, and then pushed to other devices. So you can read on your iPhone while commuting, and make highlights and notes, knowing that they’ll be visible later when you settle in to dig a little deeper while reading on the iPad. And if you need to collect those notes for a larger piece, or just to ponder them further, that’s easy to do as well.

Since it’s pretty damn easy these days to take Kindle books and convert them to ePub, that seems a logical way to protect your investment in eBooks, and to be able to maintain that age old practice of marginalia.

Happy highlighting!


  1. Thanks! It helped me! I thought that iBooks is not able to sync notes in epub drm free. 🙂

  2. I have had the same experience and come to the same set of conclusions. Out of curiosity, what has been your experience removing a book from the library and then inserting a copy at a later time? Does icloud save annotations? Or do I need to preserve a new copy with annotations?

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