PMID usage in Zotero

mgrelon
Hi,

Does Zotero use the PMID to reference its documents?
I find it very convenient to search for a given reference within a library.
Is there a way to do that?

All the best

mathilde
  • enozkan
    You can manually add PMID and PMCID to the Extra field like this:
    PMID: 29377013

    But if you are already saving from Pubmed, these are auto-populated, so you have to do nothing. If you have items without PMID/PMCIDs, and want them added without typing anything, use this plugin:
    https://github.com/retorquere/zotero-pmcid-fetcher

    I believe there are plans to give PMIDs their own dedicated field, and then the values in Extra would be automatically migrated to the field when it becomes available. Not sure.

    To search using PMIDs, just search in your library as you would normally search in the search box at the top of the Zotero window, but in the All Fields and Tags mode.
  • mgrelon
    Hi,

    Thanks a lot for your answer. The plugin is installed and works fine! that is very efficient but requires that each PMID is added individually...

    It seems that there is a way to automatically recover the PMIDS/PMCIDS by adding a new key in the preferences of Zotero:
    " extensions.zotero.pmcid.auto"
    as said here https://github.com/retorquere/zotero-pmcid-fetcher

    But unfortunately, when I did that I cannot make the PMCIDs/PMIDs appear "magically" as sold!
    They are not in my zotero item list...and I don't know how to make them appear

    if you or anybody has a clue, it would be great!

    Cheers
    Mathilde
  • enozkan
    I just checked the auto key, and it works for me. Within a few seconds of deleting PMID and PMCIDs of any item from the Extra field, they get repopulated.

    As a quick sanity check, you are looking at the "Extra" field when you said "They are not in my zotero item list", right?

    Also, the pmcid-fetcher works for items with DOIs. Does this item have its DOI listed in the Info pane (under Language for a Journal Article)? If not, add the DOI, and see that helps.
  • enozkan
    @mgrelon But you are right. It does not auto-update an item, unless you change something in the item, or add it as a new item from a source that does not provide PMID/PMCIDs.

    I see this is mostly useful at the moment of adding new items or updating them.
  • mgrelon
    Yes exactly.
    Anyway, thanks a lot for your comments. They have been very helpful.
    All the best, M
  • enozkan
    No problem. I think most of these issues will be resolved when Zotero turns on metadata updating (which is apparently already implemented and may come relatively soon).
  • rkaplan@umrpc.com
    Is there any way to automatically populate the URL field with the corresponding Pubmed page for a PMID when the PMID exists under Extra?
  • adamsmith
    No, but what's the use case? In a citation style, at least, you can easily construct the PMID-based URL
  • rkaplan@umrpc.com
    The use case is to use Aria AI to create a table which includes hyperlinks to the Pubmed page.

    It is possible to include the instructions to create the Pubmed URL in the AI prompt but the result is not consistent and it would be a lot easier to simply refer to the URL column

    A similar/related use case occurs when using Notero to import items into Notion
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