iPad Workflow: Zotero + Zotfile + ZotPad

There has been some great discussion on HASTAC about working and writing with an iPad, such as Don and Annette’s recent posts. As I mentioned in a comment on Annette’s post, I’m a big fan of Zotero for managing citations and PDFs on my laptop. For me, the fact that it does most of its work in the browser and automates downloading, moving, and renaming PDFs is more than enough to overcome some of its shortcomings. Also, it’s totally free, actively developed, and has a solid online user community.

The one big drawback to Zotero is how it handles PDFs once it downloads them. By default it moves them to a storage folder buried deep in your hard drive, and while it’s possible to move that folder into your Dropbox, it still retains Zotero’s convention of nesting your files within randomly named folders, like “3B329KFK.” Ick. The solution to this problem is Zotfile, a plugin for Zotero that allows you to choose where your files are stored and how they get named, without deep folder nesting. It does this by “linking” the citation entry in Zotero to the file. This doesn’t change the user experience at all, but just points Zotero where it needs to go. In my implementation, all of my files are stored in a folder called “Academic Research” that lives in the top level of my Dropbox folder. And the naming convention I use is “Author Last Name - Article Name (date).pdf.” Easy enough.

The advantages to this are many, but one of the biggest is that you can now sync this folder directly with any iPad annotation app that can connect with Dropbox. This includes GoodReader and iAnnotate, among many others, which can then upload any changes back to your Dropbox. Because Zotero is now linking to these files, your annotations will now be reflected back in Zotero when you open it again. As cool as this is, I was still slightly unsatisfied. I love iAnnotate’s editing capabilities, but I’m not crazy about its interface. Its search functions are limited if you don’t have your research folder fully synced, but mine has a lot of files and I don’t want it taking up precious hard drive space. Plus, iAnnotate has no way to view Zotero’s citation database, and there isn’t a native Zotero app.

Enter ZotPad, an app designed, as the name would suggest, to give you access to your Zotero library on your iPad. On Friday it was updated to version 1.2, making it much more robust as a PDF management solution. Though this release is just an incremental build over its predecessor (which was reviewed in Profhacker), this new version has significant changes, and makes it much easier for users who have a Zotfile + Dropbox setup.

To get this set-up to work, you really only need to make sure that your ZotPad preferences exactly match those in your Zotfile preferences. This is handled in ZotPad in a section called “Advanced Dropbox Settings.” Make sure you allow full access to your Dropbox, then set your naming conventions with the correct syntax.

Make sure your ZotPad preferences (left) match your Zotfile preferences (right)

Make sure your ZotPad preferences (left) match your Zotfile preferences (right) [click to enlarge]

From there, your linked files can be downloaded directly from Dropbox. You can then use the “Open In…” function to send them to your PDF editor/annotator of choice. When you are done, repeat the process: “Open In…” and send back to ZotPad, which will recognize the file and update it on the Dropbox server. It’s a robust system that really meets my needs, and doesn’t tie you in to any particular annotation software.

If you use this system and have thoughts about it, or if you have any other comments or questions, hit up the comments!

Note: Very recently, Zotfile released an update that allows for wildcard naming rules, allowing you to skip sections of your naming conventions when those fields aren’t present in your Zotero data (for example, skipping “author name” for an newspaper article with no listed author). ZotPad currently does not support this, but when I asked the developer he said it would be implemented in version 1.3.