Duplicate citations


I've just merged two documents, both with citations created via Zotero 5. Nevertheless, on refreshing the bibliography some papers are cited twice e.g. number 1 and number 5. The paper is the same, the citation the same, there is no duplicate in my Zotero library, yet Zotero has allocated two different citation numbers? Why has this happened?
  • When you click the Open in My Library button in the citation for each item, does it take you to the same item?
  • I'm not sure I have that button? Zotero for Mac, Word 2016?
  • When you edit the citation, if you click the blue bubble for the citation, you see the fields for page numbers, affixes, and that button.

    See Customizing Cites here:
  • Thanks - so in one document this button is visible and goes to correct item. In the other, the button is not visible? Does that mean that document isn't linking properly to Zotero?
  • Okay, so what that means is that the one without a button is an "orphan" citation that isn't linked with Zotero. This is likely because it was linked with an item in Zotero that you deleted, rather than merged (it could also be a version that was inserted by another author on the the document). In any case, just replace all of the instances of that version of the citation with citations to the one that is properly linked with Zotero.
  • That's exactly what it means, yes. It just draws on item data saved in the document.
  • Thanks for this - I am concerned this is just one instance when I noticed this problem. Are you working on a fix to identify unlinked citations automatically? It is concerning this could very easily go unnoticed.
  • Is there a way to search for / highlight any citation that is not linked correctly to Zotero in a document?
  • edited October 6, 2017
    It’s generally not a problem, as the document can generate references using the data embedded in the document. So I really wouldn’t worry too much here. And you should almost never end up with orphaned references at all in the course of normal Zotero usage.

    There is not currently a function to identify orphaned citations.

    @rmzelle Does Reference Extractor do this at all?
  • edited October 6, 2017
    No, Reference Extractor doesn't touch the local or online Zotero library at all, and as far as I'm aware the document itself holds no information that gives a hint as to which citations are orphaned. You could probably query the API or logged-in online library somehow with the extracted item IDs, but that's above my pay grade.

    (@bwiernik, that's also not my handle here :) )
  • I do think we need to think about a proper solution for this. It comes up too often. The Word add-on is the right place for it -- it's unreasonably complicated for an external tool as Rintze points out.
  • I have a lot of these unlinked citations. I think they came in because I pasted paragraphs containing citations from a document that I created on another computer with an older version of Zotero with a DB on that computer.

    I agree it would be nice to identify the unlinked citations, even nicer to help semi-automatically re-link them. By "semi-automatically" I mean that Zotero could relatively easily be programmed to show old and new author, date, title, etc., then ask me to accept the match. This would be a lot like the merging of duplicate records in the library.
  • I have concluded I should start at the top of my paper and check every citation to see whether it is linked or not. I originally took the entire paper off another computer that had a local DB on it; the fact that I pasted in some such paragraphs now looks like a red-herring; every citation in my paper needs checking because all the citations started out unlinked. At least now I know how to check; too bad it's all tedious though.

    Given the large quantity of citations that are unlinked, it would be convenient if I could relink them en-masse, with a GUI similar to the Duplicate Items pane in Zotero Standalone.

    Sometimes after deleting an unlinked citation, when I start replacing it, I am given a list of possible references based on the words I type into the Add/Edit Citation bar. I sometimes see two possible choices in the Cited section--one with the author's name, and the other without the author's name. The trick is that to insert the first linked citation, I need to select neither of those, and instead go down to the My Library section and select that one. For ensuing citations, I need to select the choice from Cited that includes the author's name. It took a little trial-and-error but I think I have figured out the workaround steps for now.

    Yes, @adamsmith, a proper solution would be very convenient for me.
    Thanks so much! :)
  • After systematically checking enough of my citations, and replacing unlinked ones, I no longer am presented with multiple Cited choices of the same reference. Now only the one showing the author's name is presented in the Cited section of choices.
  • I third this sugggestion.

    We really need to a solution that does the following:
    1. identify unlinked citations
    2. automatically re-link them to the knew library.
    3. identifying citations that are linked but have been overwritten manually in word. THe underlying citation has something different stored than what is written in word.

    I'm currently editing a paper (another person's) which has over 300 citations....figuring out which is linked and isn't is a nightmare
  • Hey, is there an update on this issue?
    This happens to me when I get a draft back from a collaborator, and many (but not all) references become orphan, although they are still in my library (unaltered in any way); it's just that the link is broken.

    This issue is especially annoying, as some instances of the same ref are orphaned, while any new references I make are not. This leads the citation engine to use a and b to disambiguate. So (Shahar, 2015) becomes (Shahar, 2015a) for the orphan ref, and (Shahar, 2015b) for the new/linked reference.
  • edited September 16, 2020
    @michael.pinus: I'm not sure what sort of update you're looking for. There's no bug in Zotero here. If this happens, it's something that you or your collaborator is doing. From the sound of it, they might be inserting the same citations from their own library, which creates completely new citations with no connection to the existing ones, causing Zotero to need to disambiguate the items.

    If you're working on the same document together and citing from your own personal libraries instead of a shared group library, you'd want to be sure to choose from the Cited section of the search results in the citation dialog for any existing citations rather than choosing from your library.

    You can toggle Word field codes and look at the URLs in the code to see what's going on under the hood. If my guess is right, you'll see URLs from two different users/groups for citations that are being disambiguated.
  • @dstillman -- but this comes up a ton and it's very time consuming to troubleshoot for us and to fix for users. It's technically a user error of sorts, but imo it comes up too often to be acceptable.

    An option to help relink citations would be, I think, of enormous value. I'm thinking of something along these lines:
    1. A button that highlights all unlinked citations in the current document
    2. An option to attempt to relink them, using metadata in those references to query the local library (or a group to be specified)

    I understand that the UI/UX here is not at all trivial, so don't want to minimize the effort, but as I say above -- it'd save a ton of time all around.
  • @adamsmith: Sure — I'm not saying we can't improve things. I'm just clarifying that it's not like when you get a draft back from a collaborator you should just expect to have all citations be disambiguated duplicates. If that's happening, there's something wrong with the workflow.
    I'm thinking of something along these lines:
    1. A button that highlights all unlinked citations in the current document
    2. An option to attempt to relink them, using metadata in those references to query the local library (or a group to be specified)
    Virtual collections might be the way forward here. I'm not sure we've ever thought of them in this sort of context, but they would be a good way to show a sorted list of items in the document, show which items exist in local libraries, provide a natural place to relink them to a single item, copy orphaned ones back to a library, or even edit the embedded metadata directly without relying on a library.
  • I would like to support @adamsmith in this. I have been using Zotero a lot over the past years. I removed duplicate citations from the database. I regularly copy references from old work to new documents. I just noticed this causes problems if the citations are orphaned.

    I checked an old document I wrote in 2015. It holds 50 citations in its bibliography. With Reference Extractor I found that 48 of those are in my library. However, Reference Extractor does not show which are the two that are not and need to be updated. So, if I copy citations to a new document, I have to check every single one of them to find the 1% that is orphaned and probably has a better reference in the library.
  • I removed duplicate citations from the database.
    To be clear, this is fine — you just need to merge them so that Zotero can store a link rather than deleting the duplicates.
  • It is not that easy. The different versions are not always complete, contain slight differences, I found merging is not always easier than editing one and deleting the other.
    The only thing I would like to have is to know which references in the bibliography are also in the library, and which are not.
    If you use the "Add/edit bibliography" button in Word you get a table of all references. Wouldn't it be easy if you could highlight all of them that are part of the library?
  • edited November 19, 2020
    Merging lets you choose a base version and even choose between different individual fields from the different versions.

    Providing better ways to identify orphaned citations in a document is planned, but that doesn't change the fact that you shouldn't delete duplicate items you've cited — you should always merge them. You don't have to do that, but you should recognize that you're then not using Zotero as intended and some things will work worse than they need to. There's no way that ending up with an orphaned citation in a document that needed to be fixed later — no matter how that was made possible — would be easier than avoiding the problem to begin with.
  • I'm not 100% sure if this is what you guys are talking about, but I THINK this might be related....
    When I go to "duplicate items" tab on the left, it goes through and selects the duplicate items. But if one of those items is a webpage and the other is a journal article, It gives a message that I can't merge citations of different types. Because both are highlighted by the forced default, I can't select the webpage duplicate independently, in order to drag it into the journal article citation. In order to do this, I have to go to their collection or do a full library search to locate them again and THEN merge the two of them by dragging the webpage citation into the journal article citation.

    Minor inconvenience but would love to figure out a way around it.
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