PMID automatic retrieval for existing citations

BrunoBiagianti
Hello there,

I usually add citations to my Zotero library by using the magic wand and entering the DOI. I recently submitted a manuscript to the Journal of Medical Internet Research, and they caught an oversight, which is that for some citations the PMID wasn't listed.
Went back to the library and realized that the PMID info was not always automatically entered in the "extra" field for some citations . Anything I can do to batch-retrieve PMIDs for these existing references?

Thanks!
  • adamsmith
    no, sorry. We don't have any code that allows you to update existing references at this time.
    I do hope this will happen relatively soon, but at least my guess would be that even then it wouldn't start with pubmed (though I can see the utility).
  • sidies
    I agree this would be very useful. Has this work started now?
  • bwiernik
    edited June 19, 2018
    I have written a plugin to do this for DOIs. It would be possible for someone to adapt the code there to write a similar plugin for PMIDs.

    https://github.com/bwiernik/zotero-shortdoi
  • adamsmith
    No, sorry, not started, but getting closer. Everyone agrees it'd be very useful, though.
  • enozkan
    This is especially useful for Pubmed-related entries, since they may start as advanced online publication entries (which are deposited to Pubmed soon after a paper is accepted) without details such as printed volume, issue, page number, etc.

    After the article is published in print, those values are updated in the Pubmed entry. That could be months later. So, much of my library, which was generated when the articles first became available on journal sites/Pubmed, lack these data (volume and page numbers are quite necessary, I'd say), unless I re-create the item later from Pubmed.

    I am not sure if advanced online publications is mostly a feature of biomedical publishing, or if it happens in other fields as well. But I assume that Pubmed users are generally afflicted with this problem.

    (Another issue, unrelated to the thread, is the online publication date vs. the print publication date, which can be different. Not sure what to do with that.)
  • sidies
    I've installed bwiernik's plugin (see above), which works beautifully for DOIs. Thank you very much indeed!
    I'm afraid I lack the necessary skill to adapt it. I have tried making a python script to search for PMIDs through the NCBI API, but I found that the NCBI ID converter (https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/) doesn't always find the PMID for a given doi, even when a search through pubmed's main interface does find the same PMID.
  • Martin Laclaustra
    Finally this is available through the following plugin:
    Zotero PMCID Fetcher, by Emiliano Heyns.
    https://github.com/retorquere/zotero-pmcid-fetcher
    (https://www.zotero.org/support/plugins)
    That plugin had also trouble not finding PMID for non PMC articles, but now it is fixed and retrieves all PMIDs beautifully.
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