Annotation software that doesn’t suck

Since as far as I can remember I underline and annotate my books, over the years I have developed a notation of symbols and underlining styles that allow me to highlight the passages and know the reason why that was important to me at the time by simply just browsing the book quickly. It has worked for me for texts on paper carriers for years and never had a problem with it.

For the last years a lot of the reading I do happens in front of a digital device and I have yet to find a good way of keeping notes in them. By keeping I mean, not only collecting them temporarily but keeping them across devices for a very long long time, notes that go with me and my collection of texts as my devices age and get replaced by new ones. The lack of a good way to do this is my deepest frustration with reading in digital devices.

I generally read for two reasons: research and leisure, about 80% of my reading is research of some kind and the ability to take notes is absolutely crucial to this kind of reading. If a device or reader software doesn’t include a decent annotation feature I will not even consider buying it.

I read ePUB books, PDFs, scanned documents (generally in PDF), articles on the web (html) and my annotations include a chunk of the material I am reading and a brief note, or simply just a highlight. I also like to include images in my annotations when I am researching more visual topics. Oh, and code too.

One would assume that with the Cambrian explosion of digital readers, tablets, smartphones, phablets, etc. Someone, somewhere would have come up with a decent software to annotate digital texts, but I have yet to find one that satisfies my requirements.

Here’s what I need:

  • Highlight text (with precision [you heard that touchscreen Kobo?])
  • Be able to quickly enter an annotation on the section highlighted
  • Be able to search through my notes AND through the annotated text, hopefully with the option to exclude the rest of the non-annotated text
  • I need to create my own taxonomy of annotations by means other than the document that first inspired the annotation. Tags could work for this. When researching a topic you often need to read multiple documents in various formats and I would like to be able to browse my notes by topic. Sometimes a single annotation can belong to different topics.
  • I mostly use a macbook, an Android phone and a Kobo e-reader. I have to be able to use the annotation software seamlessly across devices, and if a text exists in duplicate in more than one device I should be able to summon the same set of notes
  • I need to be able to “clip” sections that might possibly contain images and annotate those too
  • If I read a paper from its original author in PDF format and annotate that text and then it turns out that the same article gets published somewhere else in a web magazine I want to be able to summon my notes from the original and match the republished version in as far as it is computationally possible to do so
  • Every note that I take must be immediately backed up in a non-proprietary human-readable format that I can extract from the device, download or copy for free at any time. Non-compliance with this is a deal-breaker for me. I’m am tired of having my annotations locked up in some undocumented file somewhere in the application partition of some Android device, or worse yet in some SQLite database somewhere My annotations are not “application data” they are “my data”.
  • I must be able to tell the software where to store my notes remotely. I don’t want the company behind Kobo, or Google, or Dropbox or any other of these companies to have access to my thoughts under any circumstance. My notes should be dissociated from any account on any service. The only two selectors I should ever need to look up my notes on anything are, my email address and the annotated document (or some other element of my taxonomy).
  • Ideally it would be great to be able to share individual annotations with others as long as it is entirely within my agency to specify what, where and when is shared.
  • I have about eight digital devices and I have tested dozens of reader softwares through the years and I still have to find one that implements four or more of these features. Anything short of what is listed above will not cut it for reading anything that is not just holiday novels.

    Here’s a list of traumatic experiences I have had with digital readers:

    In 2013 Samsung decided to stop supporting the default e-book reader on their tablets, which was quite good actually. I learned about it after a system update wiped the reader application from my tablet along with years of annotations. Nobody in the support team could tell me where the annotations had been stored.

    The Kobo touch that I do a lot of my ePUB reading with is an excellent reading device but it sucks to take notes with. The touchscreen is not very precise so letters, words and sometimes even lines are missing from an annotation because finger-fiddling with the thing drives me nuts. The annotations are stored on a SQlite database in the device that I backup automatically every time I plug to my laptop. I had to write my own script for this. I also have another script that reads that SQLite database and extracts the annotations to HTML. For this whole workflow I had to install SSH on my Kobo, write a good bunch of scripts and hack my way through every step of it. The average consumer cannot do this.