Corrected JMIR citation style for Mendeley desktop


100 out of 100 academics agree that working with Endnote is about as enjoyable as putting your genitals through a rusty meat grinder while listening to Justin Bieber’s greatest hits at full blast and being waterboarded with liquid pig shit. I’ve spent countless hours trying to salvage the broken mess that Endnote leaves and have even lost thousands of carefully cleaned and de-duplicated references for a systematic review due to a completely moronic ‘database corruption’ that was unrecoverable.

Thankfully, there is an excellent alternative in the free, open source (FOSS) form of Mendeley Desktop, available for Windows, OS X, iToys and even Linux (yay!).

One of the big advantages of Mendeley over Endnote, apart from it not looking like the interface from a 1980s fax machine, is the ability to add, customise and share your own citation styles in the .csl (basically xml/Zotero) markup. While finishing my last revised paper I found out that the shared .csl file for the Journal of Medical Internet Research (a staple journal for my niche) is quite off and throws random, unnecessary fields in the bibliography that did not conform to JMIR’s instructions for authors.

The online repository of Mendeley is pretty wonky and the visual editor isn’t too user friendly, so I busted out some seriously nerdy h4xx0rz-skillz (which chiefly involved pressing backspace a lot) .

Get it.

Well, with some judicious hacking, I present to you a fixed JMIR .csl file for Mendeley (and probably Zotero, too). Download the JMIR .csl HERE (probably need to click ‘save as’, as your browser will try to display the xml stream). It’s got more than a few rough edges but it works for the moment. Maybe I’ll update it some time.

According to the original file, credits mostly go out to Michael Berkowitz, Sebastian Karcher and Matt Tracy. And a bit of me. And a bit of being licensed under a Creative Commons Attribution-ShareAlike 3.0 License. Don’t forget to set the Journal Abbreviation Style correctly in the Mendeley user interface.

Oh, I also have a Mendeley profile. Which may or may not be interesting. I’ve never looked at it. Tell me if there’s anything interesting there. So, TL;DR: Mendeley is FOSS (Free Open Source Software), Endnote is POSS (Piece of Shit Software).

Update: A friendly blogger from Zoteromusings informed me in the comments that I was wrong: Mendeley is indeed not FOSS but just free to use, and not open source. Endnote is still a piece of shit, though. I was right about that 😉

8 comments on “Corrected JMIR citation style for Mendeley desktop

  1. adam.smith says:

    One comment and a request:

    The comment:
    Mendeley is fine software, it’s free to use, but it is not FOSS. Mendeley is almost entirely proprietary code and, other than with FOSS software, you have to agree to a EULA before using it. There are three components of Mendeley that are open source: The CSL styles themselves (provided by an independent project), the CSL processor, citeproc-js (the same as in Zotero, provided by an outside developer), and the visual CSL editor (developed by Mendeley together with Columbia U libraries).
    If the FOSS aspect isn’t terribly important to you that’s OK, of course, but if you value FOSS software, you should take a look at Zotero, which is entirely AGPL (i.e. free/open) licensed.

    The request:
    As one of the co-maintainers of the CSL repository, I’d appreciate it greatly if you’d consider submitting your fixes to the CSL repository so that all Mendeley, Zotero, etc. users benefit from them:

    • Robin says:

      Wow, someone actually reads my blog posts?!

      Thanks for your comments, I’ll change the post. The new CSL is just a temporary patch so I can resubmit a paper but I’ll improve it and then submit an all round usable version to the repo!

  2. Maarten says:

    May I also add that both the original as your corrected JMIR template applies an ‘et al’ for 6+ authors in the bibliography, while afaik in JMIR it is common to list ALL authors. Frankly i cannot find a clear mention for this in the instructions for authors quickly though but just something i remember from ‘h4xx0ring’ the Numbered template in Endnote. So perhaps you can get away with it 😀

    • Robin says:

      Well my manuscript was accepted without a problem so… They don’t care either! 😀

      • During production, our typesetting scripts try to find the cited reference in PubMed and will make corrections automatically, i.e. substitute “et al” with the missing authors. In other words, you can list “Mickey Mouse” as author, and we will still publish it correctly, in particular if you mention a PMID in the reference (greater chance for mapping). The only thing is that the reviewers may be confused if you list “Mickey Mouse” as author, so being as accurate as possible in your review version has its benefits…

        • robin_k says:

          Hi Gunther, thanks for the clarification. It’s been a long while since I’ve changed the citation style (probably 2014 when I was working on my last JMIR paper) so I haven’t really done anything since then, and I’m sure production processes at JMIR have been steady optimising during those years.
          Matching with PMID is great, I use that feature in Mendeley all the time (although it tends to throw up errors every now and then – matching to the wrong paper). It does get more useful metadata than matching with DOI, which often fails to resolve.

  3. Dave says:

    Thanks for creating this. Saved me hours of fiddling with the CSl editor. Hope you don’t mind if I let other people on the Mendeley forum know this exists.

    • Robin says:

      No worries! No guarantees either, though. There are bound to be some more inconsistencies here and there (both in Mendeley and in my edited file) 🙂

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