Downloading a NCBI collection.

Hello.

This is on a mabcook 2014 with bigSur.

When I search the internet, all guides about importing an entire NCBI collection at Pubmed state that I should choose:

Send To -> File -> Format -> XML -> Create file

For example, in this link:
https://answers.hshsl.umaryland.edu/faq/154636

But when I push the Send To button I can only choose:
- Clipboard
- My Bibliography
- Collections
- Citation Manager

Citation manager is the only thing I can choose which export af file, but that is a .nbib file only readable by endnote. I guess I could first import the collection into endnote and then into zotero but that seems cumbersome.

If I try to select the document in the browser in the right corner, zotero imports a file or something into zotero just called 'My NCBI Collection #xxxxxx' instead of all the documents. My collection is of almost 700 citations so I would really not want to go through each one and click the the document in the right corner at each.

Any solutions?

Sincerely

  • The guidelines you're referring to are likely for the old interface. I don't think Pubmed has a GUI export to XML anymore.

    Zotero does import .nbib files, though -- it just doesn't intercept them on download, so you'd have to download the file and then use import from Zotero.
  • I confirm that PubMed no longer has XML via the GUI. They say that format wasn't well used. Please use the Feedback link to ask that it be reinstated with the new web interface.

    I have (paper-cut level) problems with the nbib files. Extra spaces regularly appear throughout the article titles and abstracts and sometimes in the journal name and even author names. Also the ISSNs require a lot of editing. See: https://forums.zotero.org/discussion/86525/nbib-import-request#latest

    I've returned to saving multiple PubMed records as PMIDs, saving them to a text editor, and using the Magic Wand to import the PMIDs three-at-a-time into Zotero. (More than 3 will result in PubMed silently omitting records -- see also https://forums.zotero.org/discussion/84985/new-odd-result-when-importing-pmids-with-magic-wand#latest

  • adamsmith:
    I was not aware Zotero was able to import a .nbib file. Thank you! The confusion stemmed from that when clicking on a .nbib file, macos doesn't allow zotero to open the .nhbib file. I had to import the file from zotero instead.
    Thank you!

    DWL-SDCA:
    That's a bit confusing when all guides on zotero is suggesting using an XML.
    Until further it works for me that zotero can import the .nbib files. I will return to the liniks you provided if I encounter said problems.
    Thank you!
  • edited December 21, 2020
    I will reinforce the idea that Zotero _perfectly_ imports PubMed's nbib file. My problem with nbib files is that PubMed creates the file with mildly annoying flaws.

    edit NLM support have acknowledged the issue with randomly inserted spaces and promise to fix that (but not soon). They also acknowledge my complaint concerning the journal ISSNs (see above) but have no plans to adjust that part of the nbib file creation.

    Maybe this is Zotero-related after all:
    Import into Zotero via Magic wand results in an issn = 1664-2295

    Import from the nbib file results in
    issn = 1664-2295 1664-2295 1664-2295
  • (happy to look into the ISSNs; please start a new thread for that)
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