Setting up Zotero to work with Dropbox and iAnnotate for iPad


Choosing a bibliography manager can be difficult, as there are many different programs to choose from. Luckily, there are many articles and blogposts that compare them. For me, Zotero came out on top. The challenge that I faced was integrating Zotero with my already existing folder structures on my Mac, as well as with Dropbox and iAnnotate.

I had previously set up folder structures per academic topic, sorting these into subcategories using subfolders. I had used Dropbox for this, in order to be able to access my library and read my files from multiple devices. In order to be able to annotate articles and books, I downloaded iAnnotate for iPad. This application enables you to set up various cloud storage services, allowing the user to open, annotate and save articles on iPad, while making these updated files available on other devices through cloud services.

This had all been working smoothly for me, until I decided it was time to start using Zotero as my bibliography manager. Using this Zotero has multiple advantages, among which making inserting citations easier, and being able to makes changes to citation styles and bibliographies quickly, instead of spending hours or  days performing this tedious task.

The first challenge I encountered was getting my head around the fact that Zotero was now the main structure through which I accessed my digital collection of articles and books. While this may sound strange, I really needed to get my head around the fact I had been using and navigating folder structures to locate literature for so long, and I now had to open Zotero to find literature instead of using Finder.

Secondly, if you haven’t used a citation manager from the very start, you will have to import your existing library into Zotero. Although you can easily retrieve metadata for files through Zotero, there will be many files that aren’t recognised. You will need to import the citation data for these files manually, for example by using Google Scholar. Luckily, Zotero has got a range of plugins that can significantly speed up this process.

After importing my entire library into Zotero (which did require me to purchase unlimited storage on Zotero servers), I realised that my old set up with Dropbox and iAnnotate was no longer working. Initially, I had come up with the idea to place the default Zotero folder in Dropbox, thereby always creating a back up, while still being able to access the files from my iPad using iAnnotate. However, it turns out that placing your Zotero folder in Dropbox is a bad idea, as this can corrupt your library. Luckily, there is a workaround for this: setting up a symlink. Simply stated, this allows you to sync your Zotero library with Dropbox, without anything getting corrupted.

The next difficulty I faced was being able to access my Zotero library from my iPad, allowing me to make changes with iAnnotate and saving them back to the Zotero server and Dropbox. Although you can access the synched Zotero folder in Dropbox on iPad, the folder structures aren’t user-friendly, making it difficult to locate items you are looking for. I soon discovered that your Zotero library is accessible on iPad by using Zotpad.

However, although Zotpad allows me to open and read documents in my Zotero library, it does not enable you to make annotations. While you can open files from Zotpad in iAnnotate (after downloading the file in Zotpad and choosing “Open in…”) the Dropbox synching option previously used in iAnnotate refers to the old folder structure that is now replaced by Zotero.

The workaround for this is to tap the tab of the file you are annotating in iAnnotate, choosing “Share…” followed by “Open in…”, and then selecting “Annotated”, after which you can choose “Zotpad”. This will place the annotated file in the upload queue, synching it to the Zotero server and Dropbox, saving it and making it available on other devices.

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