How to make Zotero even better with Zotfile

My love for Zotero is great, but even I have to admit that it’s not perfect. Thankfully, a third-party plugin called Zotfile makes up for its minor limitations with PDF management. Here are the two features I’ve found particularly beneficial.

1) Extraction of highlights and annotations from PDFs

I warn you, this feature is exciting. If you open your PDF in another application to add highlights and annotations, Zotfile can actually extract and save them as an attached note in Zotero. For example, here I’ve highlighted a useful paragraph in a journal article stored in Zotero:

Highlighted PDF

Now I can right-click on the PDF and choose Manage Attachments, then Extract Annotations.

Zotero - extract annotations with Zotfile

A note has now been attached to my journal article:

Zotero linked note

And here is my highlighted paragraph as text:


As you can see, Zotfile has also inserted the page number. Even better, it’s hyperlinked so I can jump straight back to that place in the article. This is a great way of creating an article summary with all the useful bits in one place. If you’re a Mac user and want something similar that works outside of Zotero, take a look at the Highlights App for Mac.

Here’s a short video demonstrating how to install Zotfile and extract your first annotation:

2) Sending PDFs to your tablet

These days, I read nearly all journal articles on my Android tablet and annotate them using Adobe Acrobat. Zotfile allows me to easily share PDFs between my Zotero library on my desktop computer and my tablet via Dropbox. I just need to specify a dedicated directory and choose a few options:


So, you can have subfolders based on Zotero collections, or even create your own custom folders. I’ve specified that I want Zotfile to save a copy of the file before I annotate it – this means I can retain a pristine original version, without all my scribblings. You can also choose to have Zotfile automatically extract annotations when you retrieve the PDF from your tablet.

Once this is set up, I just right-click on a PDF in Zotero and choose Manage Attachments then Send to Tablet. When I’ve finished annotating it on my tablet, I choose Get from Tablet in Zotero. You can see that this item now has my annotations as an attached note, my annotated PDF, and the original PDF.


Incidentally, if you regularly share PDFs between Zotero and another application, you can use Zotfile to change the location where your files are stored:

Change Zotero file location with Zotfile

Remember, though, that your files won’t then be synced (or backed up) with the Zotero server.

How to get Zotfile

Like so many useful apps these days, Zotfile is free. They do ask that you consider making a donation to help cover their running costs, though. You can download it from the Zotfile website, where you’ll also find installation instructions.

For many users, Zotfile will improve your Zotero experience. Thank you to the developers for making our lives a little bit easier.

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