Zotero from Mendeley and manual editing issues abound...

Gwyn Jones ZMF
Hi all,
Sorry for the long post, but I’m having some problems trying to move to Zotero, and freaking out a little! Thanks so much in advance to anyone who reads or can help.
I have recently moved over from the latest version of Mendeley 1.19.3, to a fresh install of Zotero and have been using the word plugin for citations. While Zotero looks to be exactly what I want I'm have the following queries/issues:

1) I was reading about the latest problems with importing due to mendeley encrypting the local database (as outlined here: https://www.zotero.org/support/kb/mendeley_import ) but when importing I did not have any issues with importing my references- I exported all my references as an RIS file (not using the revert to 1.18 workaround) from Mendeley and then imported them into Zotero, a quick scan and it looks like all 300+ references and the pdfs I had attached came over fine – Why?

Shouldn’t this not work with Mendeley 1.19.3? I’m concerned that I’ve made some hideous error that I’m not aware of! I didn’t have any subfolders set in Mendeley, so that’s not an issue for me.

2) I am a Psychology PhD student and my referencing is either “Smith (2004) said that XYZ” or “It has been shown that climate change is bad (Smith, 2004)”. Up until now to achieve ‘name (date)’ I have been manually editing references once they go in via the MS word plugin -APA style formatting means they are input as ‘(name, date)’ which I manually edit.

Coming to the Zotero forums the advice is that this is bad – why? I don’t fully understand what it means when it is said that the ‘references won’t be able to be updated’ if I manually edit them.

Is it just that changes I make to a given reference in Zotero, won’t pull through to the word doc? Is that the only problem? I seem to be able to add the reference, edit as needed just fine and then add a bibliography as needed. Are there any problems that come from editing that I’m not foreseeing which could catch me out at a later date?

3) I have about 1/3- 1/2 of my PhD thesis written using Mendeley, which is full of the ‘manual edits’ mentioned in 2) above. When I ‘refresh’ in Zotero with the word plugin, it removes all of the manual edits made in mendeley without the warning dialogue it does with manual edits made with Zotero.

How can I avoid Zotero overwriting updating manual edits made with Mendeley? I really don’t want to go through 70 pages of literature review to update all of my references (nearly all of which will be manually edited…). Do I have any options here or am I screwed…?

Thanks again in advance!
  • adomasven
    Shouldn’t this not work with Mendeley 1.19.3? I’m concerned that I’ve made some hideous error that I’m not aware of! I didn’t have any subfolders set in Mendeley, so that’s not an issue for me.
    What you did is fine, although if you had any sort of organised collection hierarchy in Mendeley, it would have been lost, which is why using the procedure described on the mendeley import page is preferred.
    Is it just that changes I make to a given reference in Zotero, won’t pull through to the word doc? Is that the only problem?
    Yes, this is the only problem, although technically even if you make changes to references in Zotero (say author name or publication year), they won't be pulled in into the doc, because the links between citations in the doc and Zotero is lost if the library is imported from Mendeley. If you edit references in Zotero, you will need to manually reinsert those citations into the doc for the changes to be reflected.
    How can I avoid Zotero overwriting updating manual edits made with Mendeley? I really don’t want to go through 70 pages of literature review to update all of my references (nearly all of which will be manually edited…)
    Zotero doesn't recognise citations that have been manually edited while citing with Mendeley and will overwrite them, so going over them manually is the only solution. You can enable field shading in Word to make this easier. The instructions vary depending on version of Word, but on the current 365 version of Office it's under Options > Advanced > Show document content > Fields shading.
  • Gwyn Jones ZMF
    Thanks Adovasmen, that's a helpful reply that allays some of my fears and clarifies some Zotero functionality. The tip about field shading is great too.

    Could I ask how you use Zotero on a day-to-day basis (and indeed anyone else reading) in relation to the formatting of citations in your word processing software of choice?

    Is there any other way to format the citation quickly without having to actually edit the referencing style?

    Do you just stick with the citations as they are presented and write around them? Or are you manipulating the 'prefix' and 'suffix' options with each in-text citation so it can match your requirements? Again I feel like I'm missing something obvious, as 'name, (date)' formatting is fairly common...

    Thanks again!


  • adamsmith
    The way to get name-date in Zotero is currently to use the suppress author option and type the author in the text.

    Improvements for that are planned, but will probably still take a bit.
  • bwiernik
    1) Exporting as RIS is not the method for Mendeley import described at the page you link to. That page is describing Zotero’s ability to directly import a Mendeley database. This will include notes, PDF annotations, and collections, which wouldn’t be captured by RIS. I didn’t think RIS would include PDFs either—it’s possible that the PDFs you are seeing in Zotero are new PDFs downloaded using Zotero’s ability to find available PDF.

    2) The best way to get Author (Year) citations is to check the “Suppress Author” box in the Add Citation window as described here: https://www.zotero.org/support/word_processor_plugin_usage#customizing_cites and then manually type the author names in text.

    If you just manually edit the citation, then Zotero can’t automatically update that citation in the document later. For example, if you manually edit “(Jones, 2015)” and then later add a second “(Jones, 2015)”, Zotero won’t be able to manually change the first reference to “(Jones, 2015a)”. However, if you use Suppress Author Box, then Zotero can add the letters automatically. Similarly, if you manually add prefix or suffix text (such as page numbers or “e.g.,” or “and references therein”) to the citation, this would also stop Zotero from automatically updating the citation. Always use the page number, prefix, and suffix fields to customize your citations for the smoothest experience.

    3) No sorry, while Zotero can read Mendeley the underlying data in a Mendeley citation (Mendeley uses an early version of the Zotero plugin), it can’t pick up that you’ve manually edited them. That could potentially be changed in the future, but I wouldn’t expect that to happen in time for your thesis. I would recommend re-inserting the citations using Zotero as part of your final read-through process where you are doing other proofreading.

    @adomasven Could the check for manual edits be adapted to accommodate Mendeley citations?
  • Gwyn Jones ZMF
    Ah right, thanks. I wondered about suppress author, but then you lose the automaticity of names being spelled out correctly etc. Particularly with articles which have multiple/many authors.

    Food for thought!

    Cheers.
  • bwiernik
    A more automatic version of that is planned.
  • Gwyn Jones ZMF
    That's good to know - it would be immensely useful if there was some standardized implementation of it.

    Mendeley didn't have it either but it seemed perfectly okay to make manual edits, I didn't realise the trouble it could cause though!
  • bwiernik
    It would have the same effect in Mendeley, but it seems like they are less conscientious about warning users about the potential challenges.
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