Download citations from DOIs en masse



I’m a complete newbie to JabRef so forgive me if this question is rather elementary / not appropriate for the forum. I have a list of about a 1,000 DOIs that form the basis of a meta analysis i’m conducting. I’m looking to:

a) import the full citation for each; and then
b) use the localcopy plugin to download all the article PDFs in one go.

I’m struggling with the first part (a), as at the moment the only way i’ve discovered for completing this process is to individually click on each row of my bib file, click on the refresh-looking button (a circular arrow) that appears below along with other edit options, and then select DOI, then wait for 5-10 seconds, then confirm the citation and replace original. Obviously, I have a strong preference for not doing this for c.1,000 DOIs. I’ve tried selecting all articles and clicking the circular arrow button but it only works for the first article selected.

Is there a way do what I want?

Thanks in advance!


(Bernhard Kleine) #2

As far as I can see it is not possible: the DOAJ in the Websearch list stands for Directory of Open Access Journals and has nothing to do with Digital Object Identifier. Only from those organizations in the Websearch list you can do a commandline import, yet, where you could write a script to import an entry into jabref and run that script over a list of DOI IDs.
My 5 cts.

(Tobias Diez) #3

At least the second part of you question should work, using Quality > Look up fulltext documents after you selected all of the entries. However, the completion of bibtex data cannot be automated with the same level at the moment. You still need to accept each suggestion separately. Since this also an edge use case, I doubt that we will implement it in the near future. However, there are some programs that allow you to automate other programs (e.g. autohotkey). I suggest you play around a bit with those.


Thank you both for your comments!

Bernhard, I would have no idea where to start for setting up a script to automate this process. I appreciate this might be a burdensome ask, but if easy and you have any pointers to get me started i’d appreciate them.

Tobias, thanks for the extra information on the likelihood of this functionality being added (i won’t hold my breath then). Unfortunately, I cannot use autohotkey as i’m on a Mac and it only works for Windows. However, a bit of research has unearthed Keyboard Maestro as a strong Mac equivalent

Thanks both, and have a great weekend


(Bernhard Kleine) #5

Actually, I have used such scripts when I was at the University and I could ask fellows from the computer department for help. It seemed very plausible then but I could not do it myself.
The repetive task (modifying thousands of images in the same way) was capsuled in a script. But since there is no way to use JabRef commandline for DOI I would not extend further. Perhaps, you may ask for this feature.

(Christoph) #6

You can easily download the citations from DOI in a bulk in bibtex. It’s just a simple HTTP Query for each DOI.

Downloading pdfs from a doi is not so easy, because every journal has it’s different file/link structure for pdfs.
That’s why JabRef has many different fetchers. It is based on the localcopy plugin.

When trying to get a fulltext pdf from a given DOI, JabRef tries several “fetchers” to check if the pdf can be found. E,g, first checking the journal site of the resolved DOI and then, ScienceDirect, Springer, ACS, Arxiv, IEEE and google scholar.