https://www.zotero.org/why

Used to be a Mendeley user during my MSc and PhD, but switched away. Mendeley had stalled quite a bit with their development (they were bought by Elsevier) and generally does not listen so much to their "community".

On the other hand, here in the Zotero forum, if you follow a bit, you can see how helpful people are, advice and troubleshooting is fast and bugfixes for the software can happen within hours/days.

Mendeley also has poor support for citation styles—they don’t have item types for many types of references (e.g., unpublished conference papers) and they have some unusual mappings of item fields. Zotero will yield more accurate citations if you need to cite something other than journal articles or book chapters.

In Zotero you simply double-click on items and the PDF opens up in your PDF reader of choice (e.g., Preview on macOS or Acrobat on Windows). Zotero will automatically sync annotations you save back to the file to other computers, and the ZotFile plugin can extract annotations and highlights into Zotero notes.

Personally, I would recommend _against_ Mendeley if your primary interest is annotating PDFs. Mendeley doesn’t use standard PDF annotation tools, so it’s very difficult to share your annotated PDFs with colleagues or to view your annotations in any program besides Mendeley. By letting you use the standard PDF annotation tool of your choice, Zotero makes it easier to share or work with your annotated files in other programs.

@inh3 You can specify that an item is a treaty in Zotero by entering this in Extra:
Type: treaty

That will be cited correctly for styles supporting treaty citation.

But then the pdf opened in my chrome browser (instead of Foxit) AND there was no highlighting! What's going on here?

As long as your PDF reader saves the annotations back to the original file (not a separate file) and you sync afterward with file syncing enabled, the annotations will be visible online and on other computers. I don't know if Foxit saves back to the original file by default.

I noticed it does not save it as a reference when dragging + dropping the pdf but rather as a 'file', if that makes sense.

By default, if Zotero can recognize a PDF, it will create a parent item with metadata automatically. If it can't, it will leave the PDF as a standalone attachment, and you can either create a parent item another way (e.g., saving from the browser or using Add Item by Identifier) and drag the PDF on top of it or, if all else fails, right-click and choose Create Parent Item and enter metadata manually (but that's very rarely necessary).

How good is Zotero in searching the pdf content?

Zotero will automatically index and search your PDFs. To use the main search bar, click the down-arrow and change it to Everything mode.

@Abohaal I have not used Juris-M much, but I think it supports most European jurisdictions pretty well. I do mostly cite international law (treaties and cases) and UN/AU/ECOWAS documents of various sorts.

One other thing: since Mendeley and Zotero use the same underlying citation mechanism (CSL), their support for legal research out of the box should be about the same, but with the important caveat that Zotero pulls in stuff from the extra field, as @bwiernik mentioned above (thanks for the reminder about this!). I don't think Mendeley has anything like that. So from a legal writing point of view, and disregarding the various issues re: data, privacy, corporate behavior, etc (which all would tilt in favor of Zotero, I'd say), Mendeley is at best equal to Zotero and in actuality probably a bit worse. (I think Paperpile, which also uses CSL, has a few more reference types baked into their interface so assuming that you use the right CSL style, it can produce proper citations equivalent to the use of Zotero's extra field. But I am guessing that Juris-M would be superior still).

That said, legal referencing is notoriously complex (hence the Juris-M fork) and I do not know if any software out there handles it flawlessly. But in my experience with "vanilla" Zotero (not even Juris-M) and for my uses, Zotero gets me 90% of the way there and the minor issues I fix manually (I also work a lot with Chicago [author-date], which requires legal sources in footnotes independently of the references cited list, which makes things a bit easier). I can only think of one time where we had to use an obscure South African legal format and cited cases from the African human rights system that it really broke down and we ended up doing citations manually.

@Abohaal: With auto-sync enabled, Zotero will sync within 15 seconds of a change you make within Zotero, and it will sync within a few seconds of a change being uploaded to the web library. It won't sync automatically if you modify a PDF outside of Zotero. I suppose we could consider kicking of an auto-sync if 1) you double-click on a PDF to open it from Zotero, 2) Zotero regains focus, and 3) the PDF has changed on disk.

When Zotero does not recognise the metadata it does not 'guess' a citation for it, but leaves it as purely a pdf? And so I have to right click and make a parent/citation for it ?

Yes, and that's by design, because, again, the best way to save items to Zotero is from the web or by identifier, not manually. So when we can't recognize a PDF, we leave it as a standalone attachment so that you can save the item another way and drag the file onto the saved item. In the rare case that you need/want to type metadata entirely manually, you have to use Create Parent Item.

Or worse, Incorrect metadata that is correct for a different article with a similar title. This happens too frequently to a colleague who uses Mendeley because of its social features. I suspect that part of the problem with Mendeley is that it crowdsources metadata from other Mendeley users who might be careless about accuracy.

edit: This problem doesn't happen with Zotero unless the source itself has bad metadata. I still see this when importing directly from Google Scholar instead of following the link to the publisher and importing metadata from the publisher's site.

1. Zotero, because YOU own YOUR databases.
2. You have control of your databases,
3. If you delete your databases by accident you're toast! Backup backup backup! You could purchase and setup a schedule backup with Macrium Reflect! OR a simple windows batch/vb script! OR just be mindful of your databases and backup regularly!
4. You can setup Zotero to move and use databases on ANY of your local drives
5. You can setup Zotero to move and use databases on a NAS (network attached storage) device and still work remotely. It's a little work, but it's worth the effort!
6. You are not required to log into Zotero to use the software, unless you save and sync your data on Zotero services.
7. Plugin's work (Browser extensions, Microsoft Office extensions, etc)
8. Zotero has a working development team and is constantly being updated.
9. You have tons of community support here if you are patient, which, certainly not Microsoft's inexperienced scripted support.
10. All of the above...



1. Mendeley YOU own nothing and have no control of any of YOUR DATA.
2. Mendeley's support is worthless.