Problems with my bibliography

jelena.vlasic
I've reported a problem that I'm having. The report ID is 2031766732. Shortly, I've corrected my citation and now I cannot change anything in my paper related to that citation. I've tried changing it, but Zotero tells me that I've modified this citation since it was generated and editing will clear my modification. OK, but then when I continue, it tells that an error occurred in editing my bibliography. please help me, it is a very important paper for me and I'm pretty low-life in these subjects. I', using Zotero standalone, 5,0 version.
  • adamsmith
    Remove the bibliography and try re-inserting it again.
    (The message you originally received is expected; try to avoid modifying citations in the document as much as possible)
  • jelena.vlasic
    Tried all sorts of solutions and none work. Well to be honest, I was so happy to discover Zotero and used it quite successfully, but I'm either misusing something or... For example, I can see that most of my citations contain month after year (and they shouldn't in Vancouver style), some journal names are written shortened and then initials (Clin Chel Lab Med CCLM): so I have a lot of corrections, and for month, for example, I've edited it in my Zotero, and now.... The problem is that I'm now spending more time in debugging and trying to fix stuff than maybe even to write all the literature by hand. Or maybe it just isn't my day....
  • adamsmith
    Sorry, I can really only help with specific questions or problems, not with general complaints. If something isn't working the way it should, we'd need a specific description of what's going on along these line: https://www.zotero.org/support/reporting_problems#provide_steps_to_reproduce
  • jelena.vlasic
    I'm sorry. OK, let me try stepwise:

    Report ID: 52344875

    In my word document, I have inserted many citations using Zotero standalone. The one I'm having problems with:
    1. IAfter experiencing previous problems, I've tried to delete the citation from the word document and Zotero.
    2. Then I added it again to Zotero: a journal article and a webpage
    3. Tried to add/edit citations in my add-in Zotero
    4. Zotero message: The Zotero field code corresponding to this citation, which tells Zotero which item in your library this citation represents has been corrupted. Would you like to reselect the item.... Choosing NO will delete the field....
    5. I chose NO - it gives me the same message over and over again
    6. If I chose YES, then it reopens my library, I chose again (and not just this article, any article) the same message again.
    7. What can I do, I'm trapped in a circle
  • adomasven
    Are you using Bookmarks to store citations (setting in Zotero Document Preferences)?
  • jelena.vlasic
    I'm not sure where Zotero Document Preferences is . I'm using that small icon on my web-browser, I think it's called Zotero connector for Chrome. This is one way. Sometimes, when I cannot get open access to journals, then I save pdf. I get from authors, and then I retrieve metadata for the article.
  • adomasven
    In Word under Zotero tab click Document Preferences and see whether Fields or Bookmarks are selected
  • jelena.vlasic
    I've checked, Fields is selected. Should I select bookmarks?
  • adomasven
    No.

    Click "Refresh" in the Zotero tab and when you get the message prompt, click Cancel. Zotero should have highlighted a corrupt citation in your document. Could you copy that citation, along with some surrounding text, paste it in a new Word document and send that to support@zotero.org with a link to this thread?
  • jelena.vlasic
    I'm not sure what does a "link to this thread means". Link to this discussion?
  • adamsmith
    yes, i.e. just include https://forums.zotero.org/discussion/69398/problems-with-my-bibliography#latest in the e-mail so they know what it's about.
  • jelena.vlasic
    Thank you for taking time trying to help me!
  • adomasven
    If you try to manually edit the "(56, 57)" entry, do you get a prompt for modified citation or corrupt field?
  • jelena.vlasic
    I'm not sure what manually means. I always try to correct it via Add/Edit citation because I have to think about future updates in counting my literature. And I get a prompt for modified citation, and I say OK, and then I select again, and then again the same message... A circle and no way out.
    As for months and names of the magazines, I don't care now, I'm aware that I'll have to correct just about everything. This was actually the real reason why I tried to modify the literature in Zotero by changing (deleting) the field on the date of the article, leaving only the year...
    By now I'm aware that I'll have to start a new document and start again with the literature....
  • adamsmith
    Just fully delete the numbers in the document in Word, no Zotero involved.

    We can deal with the incorrect citations separately -- there is almost certainly a way to get this right without you editing anywhere. If, e.g., you just don't want certain information included, that can be set in the citation style. But let's fix the document first.
  • jelena.vlasic
    Yes, that was my plan. It will take some time though. I plan to close Zotero (I have to have it open for inserting literature), remove all numbers (and having a copy somewhere so I'll know how to put it back correctly :)) and then, after opening Zotero starting again adding literature. Is this the right way?
    Or "unlink citations", delete numbers and then start again?
  • adomasven
    The excerpt that you have sent in does not appear to have any corrupt citations. If you try to edit the citations from the excerpt you sent in, do you get the corruption prompt? Or a prompt for modified text?

    If you do not get any prompt in that excerpt, it is likely that a corrupt field somewhere else is causing issues and you should run through https://www.zotero.org/support/word_processor_plugin_troubleshooting#debugging_broken_documents
  • jelena.vlasic
    You are right, I can correct it in the document I've sent. But not in my document. Now I'll try and check other steps. As a beginning, I can see that I have to close Track Change (I was hoping this is the only problem, step one :), but unfortunately, again the message (Report ID 1061975185, and one before, I forgot to write down the number). Now I'll try other steps. And let you know... Thank you!
  • adamsmith
    Yes, that was my plan. It will take some time though. I plan to close Zotero (I have to have it open for inserting literature), remove all numbers (and having a copy somewhere so I'll know how to put it back correctly :)) and then, after opening Zotero starting again adding literature. Is this the right way?
    Unless you're in a crazy rush (in which case I'd fix references after unlinking), no, that's not a good way to do this. Instead, once your issue here is sorted, tell us what's wrong with the references with some examples and we can see what can be done automatically without changing your information in Zotero.
  • jelena.vlasic
    Examples:
    1. Horvath AR, Bossuyt PMM, Sandberg S, John AS, Monaghan PJ, Verhagen-Kamerbeek WDJ, et al. Setting analytical performance specifications based on outcome studies – is it possible? Clin Chem Lab Med CCLM [Internet]. 2015 [cited 2017 Aug 19];53(6). Available from: https://www.degruyter.com/view/j/cclm.2015.53.issue-6/cclm-2015-0214/cclm-2015-0214.xml

    Problem:
    In Vancouver style (and it was the one I selected at the start) just about half of the data here an unnecessary here above (CCLM: initials of the journal, Internet in square brackets, cited.... Availabble from.... and month after the year of issues

    2. Perich C, Minchinela J, Ricós C, Fernández-Calle P, Alvarez V, Doménech MV, et al. Biological variation database: structure and criteria used for generation and update. Clin Chem Lab Med CCLM. 2014;53(2):299–305.

    Problem:
    CCLM, otherwise correct


    3. Desirable Biological Variation Database specifications - Westgard [Internet]. [cited 2017 Dec 14]. Available from: https://www.westgard.com/biodatabase1.htm
    4. Jones GRD. Laboratory analytical quality – the process continues. Clin Chem Lab Med CCLM [Internet]. 2016 [cited 2016 Nov 3];54(8). Available from: http://www.degruyter.com/view/j/cclm.2016.54.issue-8/cclm-2016-0321/cclm-2016-0321.xml
  • adamsmith
    For 1. if you add the page range (841-848) in Zotero, all the internet related stuff will go away once you refresh. The CCLM you should delete from the journal title in Zotero -- that probably should never have been there. Same thing for 2. and 4.

    There are Vancouver variants on zotero.org/styles that add fewer details even where they're available, you can also try those.
  • jelena.vlasic
    I've managed to correct and save my document! The problem was indeed Track changes option that I've used: even when I closed the option, the problem was still there. I had to Accept all, close Track changes and then I was able to make the change!!

    THANK YOU adomasven and adamsmith!

    I'm still having problem with styles though.....
    It seems like the problem is the way I get my literature. Anyway, too much data, and I don't really see how to fix it other than fixing (deleting CCLM, insert pages....) all of my 100ish references.
    Is it possible that I'm the only one having this problem?
  • adamsmith
    There's often some touch-up required when auto-importing metadata depending on how you import it. But e.g. importing directly from DeGruyter should give you page numbers even if you're stuck with the (CCLM) bit.
  • jelena.vlasic
    Yes, I realize it. Actually, now I will be paying more attention to the way stuff is saved to save myself further problems :). I'm now fixing many citations in Zotero because, as you said before, many missing pages, volumes etc. And it seems if you have that correct (together with abbreviations of journals) everything is fine. The problem is probably because I don't have open access to all journals (actually very few) so I get the articles all sorts of way.... And then I should spend some time...

    THANK YOU AGAIN!
  • adamsmith
    The best source of metadata for biomedical journals is generally PubMed, e.g.
    https://www.ncbi.nlm.nih.gov/pubmed/?term=25996384 would give you perfect import.
  • jelena.vlasic
    I agree. Now what I'm doing is retrieving articles, or the metadata using PubMed and then I add the pdf in it (for the articles I got, for example, from authors). Or just have the Pubmed citation to use afterwards...
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