PDF Annotation and Portability

I recently mentioned MarginNote as part of a list of Mac apps that I enjoy. It’s a very good app with powerful features like mindmap creation and research tools. There’s just one big problem. MarginNote does not embed annotations in a format I can use. Many other PDF annotation tools embed the content as a PDF meta layer. Opening the PDF in any other app means the annotations are still there. With MarginNote, all of the annotations are stored outside of the PDF and not generally accessible without their app.

Browsing through the MarginNote support threads, it’s pretty clear these are not important features to the developers. This leaves me to decide which I care about more, data portability or app functionality. It’s a tough call but I think I care more about portability since my annotations are for long-lived research.

While Dr. Drang likes LiquidText, the app hasn’t received major new features over the years. It’s still a very good app but they are missing document syncing and an iPhone app. I just can’t get behind an app with so little attention.

What I think I care about is text highlighting, the option to create image excepts of diagrams, and really good export of my annotations. Of course, I also want document syncing as well as the ability to use a Mac, iPad, or iPhone with these documents. This is the best way I’ve found to capture diagrams in technical books. That rules out a number of PDF editors like PDFPen, PDF Expert by Readdle, and even DEVONthink. Papers by ReadCude could be a solution but it requires an account to even open the app. Here’s what the Papers iOS app looks like on first launch.

Papers Login

I think this breaks some of Apple’s AppStore rules, but more importantly it tells me that it’s not an app that I want to use.

I guess I’m headed back to Highlights App and iCloud Sync.

Highlights is one of the original PDF annotation apps on the Mac that works the way I want to work. I know most PDF apps support basic annotations but Highlights just makes it easier to and more obvious.


Highlights has some unusual features too. The table extractor is just terrific.

The real bonus for me is how well behaved Highlights export is. There are a few options that integrate directly with apps like DEVONthink plus excellent TextBundle support.

Sharing Options

The Markdown (and TextBundle) export is exactly what I want. Here’s a good example of exporting annotations from a technical book:

Annotation Export