Dumping Mendeley for Zotero

Written on 2019-07-15

For several years, my library program of choice was Mendeley, which used to be a fantastic piece of software that perfectly fit my needs. Unfortunately, phenomenally bad management and some very dubious design choices have made it pretty much unacceptable. I've hesitated for a long time, but last week I decided it was time to take the plunge and have now switched to Mendeley's open source competitor, Zotero. Here's my first impression.

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I have to say I'm rather sad about having to switch. I really liked Mendeley. It had a great user interface, an inbuilt PDF reader and annotator, easy syncing, good web and mobile apps, and useful Word/Firefox plugins for citing/importing. In short, it was just what I needed. (Plus, it was free, and it worked on Linux.)

I first got a bit dubious when the company behind Mendeley was bought by Elsevier. My supervisor is vehemently anti-Elsevier, and I confess I have no great love for their business practices either. But practicality beats purity, and Mendeley was great – so I stayed.

Disaster struck some time last year, when I opened my library one day as usual, only to find I couldn't open most of my PDFs anymore. Like a ball in a magician's hand, they had simply disappeared! Soon I discovered that I wasn't the only user affected, and that the development team had somehow managed to push a buggy update that had mangled files all over the world.

Thankfully, I had just handed in my bachelor's thesis, or I would have been completely screwed. In my then-current situation, it was merely an inconvenience that I hoped would soon be righted. But not only did Mendeley take several weeks (!) to release a fix, it so happens that the fix didn't work on my machine. Even now, most of the entries in my library are orphaned.

As I am now back in a stage where I have to do a lot of literature research, that basically spelled the end of my Mendeley time. I can't work with a broken library, and I won't fix a library if I can't trust the hosting company not to break it again (or even to care that it's broken). So I knew I finally had to make the switch to Zotero.

As I read up on making the switch, I discovered two other things about Mendeley. First, their Word and Firefox plugins are basically forks of older (and inferior) versions of the same Zotero plugins. Secondly, a couple of months ago, they started to encrypt their library databases. With the result that Zotero can no longer import Mendeley libraries, even though the reverse is perfectly possible. In other words: Mendeley not only broke my library, they are now preventing me from salvaging it with a working program.

It turns out I still had an old backup lying around that was still unencrypted, so I have been able to recover about three quarters of my library entries for Zotero. But as you can imagine, I was still pretty upset.

So now I'm on Zotero. My general impression is favourable so far, although some things are still suboptimal. My biggest lament is the loss of the Mendeley PDF editor. For some inexplicable reason, there still isn't a decent general PDF editor available for Linux, at least not on a GNOME desktop environment. Meaning, I can no longer directly annotate my PDF files. Oh well.

Slightly bothersome was the fact that several features that I was used to from Mendeley are only available via plugins in Zotero – but at least they are available. (For example, creating a constantly updated BibTeX file from a collection requires the “Better BibTeX” plugin.) I'm also going to miss the Mendeley mobile app, although I understand Zotero has hired an iOS developer to build one. (Hope it comes out soon!)

Other things, however, are significantly better. I am especially pleased with the import process. Zotero is a lot better at identifying article metadata from the PDF file. On Mendeley autorecognition worked about half the time, on Zotero it's more like 90% – that saves a lot of effort! Also, the web importer (Firefox plugin) actually works, and is usually spot on.

I like the coloured tag system, and the ability to attach HTML notes to items. Most of all, I am relieved to know that this is open source software that I can fork myself, if necessary; and that I can sync my library using my own WebDAV server – without having to trust any external company.

To sum up: I have traded in a bit of convenience and some very useful features in the switch away from Mendeley. But given that I can no longer trust the company, I can live with that. And in several ways, Zotero really is better.

Tagged as computers, science

Unless otherwise credited all material Creative Commons License by Daniel Vedder.
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