Moving from Endnote to Zotero

A running theme of this blog (and my work in general) is in using freely available software when I can. There’s multiple reasons for this; the main and most obvious being saving money. But there are other reasons too – losing access when changing institutions (or when licensing changes and something becomes unaffordable) is a big one.

I’ve been using Endnote since I started my PhD in 2006. I’ve always been fortunate enough to get it through whichever institution I’ve been at during that time, so I’ve never actually bought it. I’ve gone from Endnote 9 in 2006 all the way through the X releases to the current X9.3.3. It works fine.

When my PhD students have started in the past, I’ve recommended them getting started with Endnote simply so we have compatibility when co-authoring manuscripts. Some have done so, while some have continued using Zotero because they were already using it.

I don’t have a lot of impetus to move, to be honest. Shifting to Zotero would mean old manuscripts of mine would be incompatible and need all the references replacing, and there’s the time sink of getting it all setup.

However, I’m just so sick of the Endnote interface which has remained basically unchanged since 2006. It’s functional, but not exactly pretty, and it’s usability is crap on a smaller touch screen like my Surface Go. I’m a sucker for User interfaces and UX, so decided that was enough reason to give Zotero a go.

If you’re already familiar with both pieces of software, you can skip to the end for info on how I made the switch.

I’d avoided Zotero for years because it was, at first, mainly a Firefox plugin. I don’t like web apps or browser-based software, so avoided it. It’s been a stand alone program for a while now, so I thought; ‘what the heck?’

It took a bit of fiddling to convert my Endnote Library and make sure everything was correctly transferred across. Zotero is just as crap on a small touch screen (maybe even worse), but does look marginally better in use. A big bonus is how easy it was to use Onedrive for storing PDFs, which was a little flaky on Endnote. I’ll give some details below, comparing both programs. Full disclosure: I’m not a power user of reference management software; I chuck my PDFs in, then I cite them in word and make a bibliography, that’s about it.

User interface

I’ve tweaked Zotero to look a little more like Endnote than it does by default. You can see from the images above that Endnote is just a bit messier. The outline-based icons don’t gel with my personal preferences, and there’s just so many of them. There’s nothing special about Zotero, but it is a touch cleaner.

Endnote does have a PDF viewer built in:

But to be honest, I don’t really use it. I much prefer to just double click and open the PDF in Xodo where I can mark it up and read it quicker. In Zotero, a double click on the reference will open the PDF in whichever PDF reader you choose.

Scrolling a large library is a little slower and jerkier in Zotero than Endnote, especially on the lower powered Surface Go. I think it’s just loading attachment status for each entry, and that involves checking the disk apparently. Turning that column off does make things slightly smoother, but not a lot. Disappointing.

The biggest difference is in the in-word UI. In Endnote, the default keystroke (on Windows) is alt+7, and on pressing it this window immediately appears whether Endnote is running or not:

You search at the top, find your reference and then double click on it. Endnote then immediately places the reference in the text, and creates a bibliography at the end of the document.

In Zotero, things function much the same way, but instead of a large search window, there’s just a search bar, and entries appear as you start typing:

I’d argue Zotero’s reference-adding interface is nicer. It doesn’t come with a shortcut key automatically though – you have to add that yourself in word (which is a minor inconvenience). You’ll also notice it doesn’t add the bibliography yet. You have to manually tell it to add or update the bibliography.

Handling different reference styles

Both pieces of software have a bunch of styles built in, and can download styles from the web. I will say that Endnote’s style editor is miles better than Zotero’s. In Endnote, you can directly edit using plain text where things go:

Editing how citations appear in Endnote
Editing how the bibliography appears in Endnote

In Zotero it’s a bloody great big XML file that needs editing directly:

Zotero’s style editor.

Whilst all the journal’s I’ve formatted for so far have had Zotero styles downloadable, I dread having to parse this to edit it.

Handling citations – removing authors, adding pre- and post-fixes.

Sometimes you want the author outside the brackets, such as if I were to refer to a work by Falkingham (2014), rather than simply to a previous study (Falkingham 2014). Or maybe you want to get an ‘e.g.’ or ‘contra’ inside the brackets. It’s pretty much the same process in each. In Endnote, you right click and edit reference:

And in Zotero you click in the reference, then add/edit:

Zotero is a little smoother and nicer looking in this process.

Storing attachments:

Both Endnote and Zotero offer online storage on their own servers, allowing you to sync libraries across computers. Last I checked, Endnote was limited to 2GB, but looking at the documentation now, it seems that the online storage is unlimited. That’s a big deal if I’m reading it right. Zotero offers 300Mb for free, or you can buy increases to that.

Here’s the big difference I’ve found though: Endnote is quite difficult/finickity to set up so that it uses external storage (Onedrive in my case, but equally Dropbox, GDrive etc). I’ve been using it this way for years (because my PDF collection is much larger than 2GB), but it involves making sure that your whole library, and all the database files are together in Onedrive, and that you never have Endnote open on two computers simultaneously or you’ll encounter locks on the database files.

Zotero is quite happy for you to sync your reference data, but keep all your PDF’s in a folder that you sync between computers. Far better.

Pros and Cons of each:

Honestly, in terms of usage, it’s six of one, half a dozen of the other. If you have access to Endnote, and know you’ll have it for the foreseeable future, I don’t think there’s any downsides to sticking with it.

I think Zotero has a slightly nicer interface, even if it’s a bit slower scrolling through a large library. It’s certainly fresher to my eyes, which have been staring at Endnote’s stale UI for the best part of a decade and a half.

I did find Endnote was a bit better for finding PDFs and updating citations for references already added. Zotero can do this fine if you have a DOI, but Endnote can do it with just title and authors.

I do think (hope?) that going forward Zotero’s going to see the most development, much like Blender seems to be rapidly overtaking Maya in usability and features. I can see Zotero making a touch-friendly interface on Windows long before Endnote ever does (I hear there are large UI changes coming to Zotero next year?).

Making the switch.

As the title of this post implies, I’ve moved my library of references and PDFs from Endnote to Zotero recently. It’s mostly a straightforward process, but I’ll outline what I did here:

Export your entire library from Endnote as an XML file. Select all your references, then go to file->export, and save as type XML. Output style should be ‘show all fields’.

Then in Zotero, go to file->import.

Only one option here…

You can choose to copy files, and it’ll find the PDFs that were pointed to by Endnote. Before I did this, I made sure that in Zotero Preferences I set up a folder structure for linked attachments. This sits in my OneDrive folder:

The data directory is in my user directory, and syncs with Zotero servers. This way, I can sync reference details across computers through Zotero, but sync the PDFs through OneDrive (where I have 1TB of storage).

I also use ZotFile ( which adds into Zotero, and makes sure that every time I add a reference, the PDF is properly renamed and moved to the right place. I have it set up like this:

In other words, it’s moving files to the same directory Zotero uses for linked attachments. The folder looks like this:

I much prefer this to Endnote’s mess, which has each PDF in it’s own randomly numbered folder:

Making the switch to my workflow:

In terms of actually making the switch to using Zotero on Manuscripts, this has been a slow process, requiring me to keep both reference managers installed, and both updated with new references I add. The reason for this is that I have (/had) several manuscripts half written using Endnote, so they needed to be finished using Endnote. But I’ve started new manuscripts, and relied on Zotero for them. I haven’t quite got to the point of uninstalling Endnote and deleting the library from my computer yet. I’ll probably give it a full year and see where the UI’s stand for both in relation to usage on my surface, then take the plunge one way or another.

3 thoughts on “Moving from Endnote to Zotero

Add yours

  1. Thanks for posting, I’m moderately intrigued. I’ve been using EndNote since Jerry Harris introduced it to me in the late 1990s. My library is over 15000 references. I’m even less of a power user than you—having gone through many times when EndNote and Word failed to keep current with each other, I usually just keep a separate bibliography document (drag references into that as I use them, then copy and paste its biblio into my ms when it’s nearly time to submit). As a Mac user I find it easier to just search on pdfs using my own protocols (e.g., Heckert2020, HeckertFalkingham2020, FalkinghamHeckert2020, Falkinghametal2020 will get results for papers by myself, myself and you, you and I, and you and others in 2020).

    If I submitted to journals requiring numbered references that might change, but it might not.

    From what I read it sounds like, as long as I get EndNote through my employer, there’s no point in changing. On the other hand, for the sake of students that might go on without access, it sounds like perhaps now is the time to switch over. The carrot I’ve offered is that they have access to my monster library—I’m glad to hear that they can export it.

    I’ll look forward to hearing more from you about this. Another thing I’m thinking about is that if Zotero is effectively the same for most users, then I won’t fight if my university decides not to renew with EndNote.

    1. I’ve found the development rate of Mendeley to be frustratingly slow, and last time I used it it had become a something of a neutered webapp. I do install it occasionally to see how it’s progressing, but it’s not software I get on with. Regardless, unless they’ve changed it, the biggest issue with Mendeley was trying to set it up to use Onedrive, rather than paying for their storage. I also know that some people have an issue with it being bought and now owned by Elsevier.

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