Inconsistent PMID and PMCID info in downloaded refs

doblk

I am writing an NIH grant application that requires PMID and PMCID in the references. I am using the National Library of Medicine citation style in Zotero, which is formatting the citations with the PMID's, when they are in the downloaded reference. However, not all the references have this information attached, even when is is available. The references are downloaded using the Zotero Firefox add on from a Pubmed page in either the summary format or medline format. Both of these formats display the PMID's, but they are not always included in the downloaded reference. Is there a way to always include the PMID in the downloaded reference?
Thanks for any ideas.

adamsmith

As long as you're importing from Pubmed, I would expect results to be consistent -- I'm pretty sure everything imported via Save to Zotero button and Pubmed XML would include PMID and PMCID. It's possible we don't have that in the Medline format, which doesn't get as much attention (because it doesn't really have any advantages over the XML).

Beyond that, we'd need specific examples and steps to reproduce.

doblk

Thanks for the response. One example reference is:
https://genome.cshlp.org/content/23/6/998

It has PMID and PMCID. When I save to Zotero from Pubmed this info is not there. I can save from either Pubmed summary format or Medline format and I get a Zotero reference. This gives me the PMID in other cases. When I save from XML format it either shows an error or saves an empty reference. So I haven't used that.

I am using Zotero 5.0.66 and Firefox 60.6.3esr, on a MBP running Mojave 10.14.4.

Thanks for your help. The grant is due today and it would be great if I didn't have to add 100 PMCID's manually.

adamsmith

When I save https://www.ncbi.nlm.nih.gov/pubmed/23636947 via the the save to Zotero button, I get PMID and PMCID -- you should typically use the save to zotero button for best results.

How _exactly_ are you importing. The pubmed website gives you lots of options.

doblk

Thanks Adam.
I go to Pubmed on Firefox, I search Pubmed for references.
I display them in either summary or medline format on the Pubmed page.
I click on the Save to Zotero button, and it shows the list from Pubmed and I click on those I want and click save.
I have Zotero already open and the references appear there.
This all works great except only sometimes do I get the PMID's.
I can also display in XML format in pubmed. But Zotero throws an error when I do that.
Hope this helps!

adamsmith

I go to Pubmed on Firefox, I search Pubmed for references.
I display them in either summary or medline format on the Pubmed page.
I click on the Save to Zotero button, and it shows the list from Pubmed and I click on those I want and click save.

OK, that sounds exactly right and should reliably work. I'd need a specific step to get me to a place where it doesn't. As in -- "I search for 'XYZ' and lick on the the third item, with the title 'ABC' and it imports into Zotero without PMID"

doblk

Well now it seems to be working. I don't think I have changed anything but downloads that did not have PMIDs before now have them. I am going back and redoing my searches from yesterday and earlier to get the full citations. Then I will merge all the duplicates. Weird but at least it seems to have resolved. Thanks for walking me through it.