How do I take a long list (approximately 1000) of PMIDs, and ask JabRef to download BibTeX citations for them from PubMed? Pasting them into the Search box does not work–all spaces are removed between them. Individual PMIDs work, but boolean does not: xxxxxxxx OR xxxxxxxx does not work (it produces no articles), and typing PMID:xxxxxxx OR PMID:xxxxxxx also leads to no hits. Though if I type “hiv or tb” in the search window, it does find articles (suggesting that boolean works in the window). This behavior is counterintuitive since these searches do work on pubmed itself. Parentheses do not help; etc. I can add a single entry at a time; this isn’t acceptable–I need to do many hundreds of these. I do not want article PDFs, just these citations. I don’t see anything in the jabref help, and am stuck in a rabbit hole. Sorry for the newbie question. Thanks.
Hi,
it’s a bit confusing for newcomers. The search box is not intended for IDs (we are about to change that)
So you would have to go the way using New Entry → And then import by ID.
But this is cumbersome.
But the easiest option for batch would be to do a search on the pubmed website, and then
Send to → Bibliography manager → Create file
And then you can import the nbib file in JabRef via File → Import
A third option is to use the JabRef Browser extension. But that will only work for visible citations on a page.
In any case, it is disappointing that JabRef does not include the abstract when retrieving articles from PubMed. The workaround I use for this scenario is to search PubMed for the long list of PMIDs, save the results, and then import to JabRef. Search PubMed like this:
1234567 9876543[uid]
You don’t need to repeat [uid] for each PMID and you don’t need quotations, commas, or the OR operator between PMIDs.
Fantastic! I am really longing for the opposite scenario too, where JabRef fetches the PMID and adds it to existing entries.
It’s not a bad solution.
Ehm, JabRef fetches the abstract. If you use the Library New Entry → Pubmed/medline and add the id, for example: 11748933 than it will also fetch the abstract
Ehm, JabRef fetches the abstract.
Indeed it does. Sorry. I got PubMed mixed up with doi.org.