Zotero: An open-source tool to help collect, organize, cite, and share research

I set it up to sync the full-texts via syncthing, has been working flawlessly.

I use Mendeley instead of Zotero. I really wanted to like Zotero, since I hate Elseveir like the next guy, but Zotero didn't have any of the look-up features and ability to quickly import my papers (thousands). In Mendeley, I can just throw a physical folder into a folder and it'll tag and categorize the PDFs mostly correctly.

I mean it is nice that Zotero has an import browser plugin (which, btw, Mendeley does as well), but once you have a substantial library of pdfs, it is just too time consuming to re-import it all again, type in names, years, journals etc. ugh..

Also, Mendeley can open pdfs within the app and has great features for mark-up and comments. Reviewing a paper is really nice this way. In fact, Mendeley is the program with the best mark-up features on all of Linux, in my opinon. And all this is synced across devices.

I'd love to use Zotero but tbh Mendeley is just better.

Your information might be outdated -- In the latest version of Zotero, when you add a PDF to Zotero, it automatically retrieves the metadata via DOI lookup.

(I don't think it would work with papers too old to have DOIs but haven't checked lately.)

I have just recently switched away from Mendeley because of an insanely user-hostile thing they've just done to lock-in their users.

Mendeley has started encrypting users' bibliography files (from version 19), claiming variously that encryption is required by GDPR (?!?!) and/or that it improves security on a multiuser system. (Neither of these excuses holds water.) The keys are not available to the users whose data were encrypted. The encryption is completely proprietary and there are no tools available for letting users work with the now-encrypted databases.

Previously, users could access their data by running `sqlite3` on a plain sqlite database in their profile directory.

Not only did users take advantage of this, but a small ecosystem of third-party tools and scripts had sprung up to help people take control over automating repetitive tasks in managing their bibliographies.

Well, now Mendeley has encrypted everything, that's the end of that. No more tools and scripts. No more user control over one's own data and workflow.

There's now only the limited (for my purposes, useless) "export database" facility in the client. It only exports a limited subset of the fields in the database. Alternatively, I could register as a developer, get an API key, and develop a full web-style app to get hold of my own data. ("Did you just tell me to go fuck myself, Bob?")

The Zotero people suspect that Mendeley's move was retaliatory for Zotero's implementation of import-from-Mendeley [1]. The Mendeley twitter account has dismissed this - literally - as being "fake news" [2]. Super weird.

I reverse-engineered the encryption they'd put in, in order to export my own data and migrate to Zotero. I wrote up the instructions for others to follow [3], but it's really not easy, not portable, not reliable, and not something users should ever have to do just to get access to their own data!

Anyway, at this point, I don't trust Mendeley as far as I can throw them, and I thoroughly regret ever recommending to my friends that they use the tool. After nine years of using Mendeley, though, I've switched to Zotero, and it's at least as good, and in some ways better. Plus it's properly open.

[1] https://www.zotero.org/support/kb/mendeley_import

[2] https://twitter.com/mendeley_com/status/1006919608471818240 and several others. Really, the official twitter responses from Mendeley to people discussing this issue were bizarrely dismissive and mocking.

[3] https://eighty-twenty.org/2018/06/13/mendeley-encrypted-db

Zotero is awesome. 80% of the academic type people I've introduced it to have switched. The other 20% have Endnote stockholm syndrome.