Deciding between Zotero and Mendeley

Hello,

I have trouble deciding between the two. It is for my law thesis and I will be working with a lot of pdfs on different computers. I want to be able to eeeeasily annotate + cite them. I tried RefWorks but it felt too slow. Everyone recommends Mendeley since apparently it is a lot snappier. What do you guys say pro/con wise?
  • I tried to use both of these tools before, but Zotero was better for me and I stopped using Mendeley. But if I have to say why, I can't answer exactly.
  • 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.
  • Zotero today is faster than Mendeley and, I think, have more features. In addition, if you are doing a lot of legal citations, you might want to look at Juris-M which is a fork of Zotero that includes additional features for legal writing.

    Neither Zotero nor Mendeley is particularly well set up for the intricacies of legal citation and neither has certain reference types like treaties that might be important to you. Juris-M adds these. I believe Zotero will get some of these in the future, but I don’t know when. (I am not affiliated with any of these programs.)

    FWIW I do quite a bit of legal writing and have to cite relatively obscure jurisdictions and for that I use Bookends and use Zotero more for collaborative writing and teaching.
  • Mendeley also has poor support for citation styles—they don’t have item types for many types of references (e.g., unpublished conference papers) and they have some unusual mappings of item fields.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.
  • edited March 26, 2020
    I appreciate all the replies. But for my purpose, which is mainly annotating and citing PDF files in a cloud, it seems Mendeley would be better since Zotero has no built in PDF annotator right? What I do like about Zotero is that apperently there are even fields for ECLI-codes of Cases. seems nice, but without being able to annotate PDF it is kinda useless.

    I read about Zotfile but that is a workaround no?

    @inh3 interesting, is that also European / civil law ?
  • 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.
  • @Abohaal Zotfile is helpful if you want to move PDFs between Zotero and an external folder (e.g. Dropbox) for purposes of reading on an iPad. I haven't done this in a while but last I did it worked quite well.

    Re: the legal stuff, I'd recommend you look at Juris-m to see if that works. The Geneva Graduate Institute also has a pretty helpful guide for how to make Zotero work for international law, which might be helpful. Personally, I tend to cite international law or specific African jurisdictions, so I do not really know about European/Civil law.

    For the more rarefied situations, I use Bookends because it allows you to customize reference types (so I have a specific reference type for treaties, one for UN docs, one each for various West African jurisdictions, and so on). As far as I know, only Bookends (Mac only), Citavi (Windows only), and EndNote (nominally cross-platform but basically unusable on Mac) allow you to customize reference types.

    But if you can make Zotero work for you w/o that, it is probably the more seamless solution (and you have the benefit of your money not going to some large corporation, unlike Mendeley).
  • 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.
  • And not only that: they encrypt their database so that you cannot migrate away at a later date. Your research data (including these annotations!) becomes entirely beholden to their whims (and quality control). For this incredibly user-hostile action, they say that they're mandated to do so by the GDPR, but have not been able to answer in over two years now which article of the GDPR would force their hand, but not Excel, Access, Word, Pages, or, in fact, Zotero.

    On a more positive note, if any of your needs include BibTeX, or RMarkdown, Zotero plus plugins (full disclosure: one of those plugins is mine) give you for free (open source even, all of it) what others don't give you at any cost.

    And I'm willing to stake money on that my support is better than Mendeleys'. Free.
  • @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.
  • Thanks for the replies everyone. You gave me a lot to consider. Now there are still some considerations I hope you guys can I help me with. Since I am not very tech-savy.

    1.a. I played around with both Mendeley and Zotero. When I drag+dropped a pdf in Mendeley Desktop and highlighted it, I could open the M-pdf via M's cloud and it included the highlight.

    1.b. When I drag+dropped a pdf into Zotero Desktop and I tried opening the pdf, it opened the pdf with my own Foxit pdf software (as expected?). So I highlighted the Z-pdf, I closed Zotero Desktop and I went to Zotero's online version to take a look. But then the pdf opened in my chrome browser (instead of Foxit) AND there was no highlighting! What's going on here?
    Also I noticed it does not save it as a reference when dragging + dropping the pdf but rather as a 'file', if that makes sense. I tried to go through the documentation but it only made matters more confusing? In Mendeley it automatically becomes a citation with a pdf (even though most of the citations are wrong since theyre not files with identifiers sometimes)

    2. How good is Zotero in searching the pdf content? I've heard Mendeley is pretty good at indexing the content within the PDF and I can easily search for the content.

    (PS: I'm not interested in possible perks they have regarding collab or sharing. It's just my own stuff for my master thesis and possible postdoc)

    @inh3 Also, regarding Juris-M, it could be interesting but since I'll mostly work with Dutch law i'm not sure if it is truly more useful than zotero, I am guessing you mostly use international law?
  • edited March 27, 2020
    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.
  • It may also be that Chrome wasn't displaying highlighting properly. I suggest opening it in a proper PDF program to be sure.
  • @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.
  • edited March 31, 2020
    @dstillman and @bwiernik

    - Regarding sync: I found out what was going wrong. Apparently my Zotero does not sync automatically after changes (not instantly). What happened was I highlighted it in Zotero Desktop but the last sync was 30min ago. Highlighting and manually pressing 'sync' works. Is there any method to make the sync 'continuous'? Because I can predict that this is going to be something I will forget hah.


    - Regarding parent items: I think I understand. 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 ?
    That's kind of annoying since for one or other reason most European national law papers seem to be almost DOI averse. Why, I've got no idea but the majority of the Dutch papers I use seem to be without any metadata.
    To be fair though Mendeley's "forcing" a citation is just a annoying, I have no idea how Mendeley's algorithm works but some of my papers got turned into Chinese/Asian script citations for one or other reason. (RefWorks seems to be the best at 'guessing' or identifying keywords for a reference, but I find RefWorks a bit sluggish in usage)


    @inh3 I looked at Juris-M, but to be honest I did not see a particular advantage (compared to regular Zotero) to it for Dutch law. Am I missing something?
  • @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.
  • 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.
    That approach also doesn't create an item with very low-quality metadata that would have to be corrected anyway.
  • edited March 31, 2020
    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.
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