Academic PDF management with Zotero

Nowadays there are a plethora of reference managers competing for the attention of academics. While each has its own pros and cons, Zotero stands out as the best tool to use for managing a digital library of PDFs. Zotero is free, open source and maintained by academics – a real advantage at time when most other reference managers are now run for profit or owned by large journal publishers. Moreover, Zotero is perfectly suited to helping you seamlessly manage your PDFs in a manner which suits you, without the potential of costly upgrades, being locked out when you change institution or the company behind the product goes bust. Just as with real books, a comprehensive, well managed and library of PDFs can both save you both time and be an invaluable resource for your research. Thankfully, when we have Zotero setup properly most of the maintenance required in curating your personal library of PDFs should be taken care of automatically allowing you to get on with the important aspects of your research rather than spending your time classifying, renaming and organising hundreds of journal articles.

The system presented in this article will setup Zotero to add the data from a journal page or library search to our library, when available download the attached PDF, rename the PDF to include details of the date of publication, journal, author and title, move the file to dropbox and create folders for each specific author. The system should be replicable across all operating systems and with the use of dropbox (or similar) allow us to maintain our PDF library on several computers or when upgrading our computers. The instructions given here will be specific to OS X, however, the procedure for other operating system should be broadly similar and intuitive.

The first thing we need to do is download Zotero itself from https://www.zotero.org/download/. We specifically want Zotero Standalone.

Having installed installed Zotero we then want to install a Zotero plugin for our browser of choice. Personally, I use firefox, as it better integrates with Zotero and it allows me to dedicate a browser purely for my academic work – making it easier to manage multiple tabs, half-read journal articles and removes the temptation to keep checking facebook (if you already use Firefox as your main browser you can always setup another copy to use for you academic work and with Zotero). That said, this is mostly a matter of personal choice and you shouldn’t notice a difference with whatever browser you choice to use.

Next want to go to our dropbox folder and create two new folders (dropbox is not strictly necessary but it allows a single Zotero library to be used across several different computers and continuously backs up our library. Of course there are other alternatives – including Zotero’s own free and paid for server space – but I won’t digress into setting those up here). The first folder can be called whatever you want, I rather unimaginatively went for ‘Zotero PDFs’, but anything will do, the key is wherever you place this folder is that it stays in place and does not move about to much. Inside this folder we want to create another folder called ‘Data Directory’.

Having created these two folders we now need to open up Zotero and navigate to the app preferences. Once there you want to click on Advanced and then ‘Files and Folders’. Then for the first option select ‘Use Relative Paths’ and select the Zotero folder we just created in our dropbox. Below that we then want to select ‘Custom Data Directory’ and navigate to the Data Directory folder we just created on dropbox. Having done this your selection should look something like this: It turns out that this is actually very bad advice as the underlying sqlite database not only eats up loads of data by constantly updating but also that dropbox’s (or any cloud storage systems) way of updating files between different operating systems is likely to corrupt your database. Instead, what we need to do is keep the local stand alone database (by making sure ‘Use profile directory’ is selected) and then use a potential workaround by creating a symbolic link from this database to our dropbox folder – as detailed here http://zotpad.uservoice.com/knowledgebase/articles/103395-what-is-a-symbolic-link-and-why-should-i-useone-w. I’ll investigate this further and update this section as necessary, but for now it looks like the easiest thing is to keep the Zotero database as local file and occasionally back it up manually or use Zotero’s own service for cloud syncing.

Having done this we then want download a plugin called Zotfile to manage our PDFs for us. While not officially part of Zotero itself, Zotfile is what makes Zotero so useful for managing our PDFs and not just our citations. Zotfile can be downloaded from http://zotfile.com/. Having downloaded Zotfile we need to install it through Zotero’s add-on manger which can be found at Tools > Add-ons. Once there you need to click on the gear in the top right hand corner, select ‘Install Add-on from File’ and navigate to the Zotfile download. If you see any security warnings about Zotfile don’t worry, it is written and maintained by a professor from NYU and is 100% secure.

Having installed Zotfile we then need to customise it to suit our needs. Click on preferences under Zotfile and you should be presented with an options menu like the one below. We then need to select a custom path for out ‘Source Folder for attaching new files’. In my setup, I created a new folder for all my downloads from firefox named ‘academic downloads’ to prevent Zotero for organising all the junk PDFs I download in day to day life, but this is simply a matter of personal preference. To change the default downloads folder go to Firefox > Preferences > General and change the folder listed under Downloads > ‘Save Files to’. Having set the folder we then want to select ‘Watch for new files in source folder’ which will allow Zotfile to automatically organise our PDFs. Below this we want to change the Location of Files setting to the Zotero folder we created on our dropbox. Below this select ‘use subfolder defined by’ and type in:

/%a, %I/

Altogether it should look something like this:

The %a and %I here specify that we want Zotfile to create a new folder for each new author that it comes across and name that folder after the authors lastname and initials. If you want you can change this setup, the different variables available are listed here http://zotfile.com/#renaming-rules. After this we then need to click on ‘Renaming Rules’ and change the entry for ‘Format all Item Types’ to:

{%a} - {%t} - {%j} - {%y}

Again this is open to personal preference, the code used here renames all PDFs to follow ‘Author – Title – Journal Name – Year’. This section should look like this:

Having done all that our system should now be ready to use! Below are a few screenshots to this system in action: