Does anyone know a quicker or more automatic way to get articles downloaded on Mendeley desktop?

October 30, 2012 9:48 PM

My boss (neuroscience professor) wants me to import all of her authored online journal articles (in PDF form) into Mendeley desktop. So far, I’ve been using PubMed to click on each article of hers, then accessing the PDFs through the specific journals (behind the paywall), and then downloading the papers one by one. Does anyone know a quicker or more automatic way to get articles downloaded on Mendeley desktop? Perhaps through an API? Also, does anyone know a way to quickly / automatically import citations that are used within an online journal article?
posted by kirsti to computers & internet (7 answers total)

As someone who goes through regular binges of adding dozens of articles to Mendeley at a time, I doubt there is a better way. But if you have set up your workflow effectively, it shouldn't take you that long to do it even if you download each paper one by one that way (I'm assuming she has no more than a few hundred articles). Do this at the institution so you don't have to log in for each journal (I hope).

1. Set up your browser so that PDFs open in Mendeley Desktop instead of Adobe Reader or the Adobe plugin.
2. Start Mendeley Desktop in advance.
3. Display all of the author's articles. Search PubMed for, say, West JC[au] if her name were J. C. West.
4. Display Settings. Format: Abstract, Items Per Page: 200
5. Scroll through and Ctrl+Click on each full text link in order. This will open a new tab for each article.
6. Open the PDF from the full text link, if necessary. It should be loaded straight into Mendeley Desktop.
7. Sync.

Also, does anyone know a way to quickly / automatically import citations that are used within an online journal article?

Do you mean you want to add a Mendeley Desktop record for each article that a given article cites? So for 100 articles times 30 citations, you would have roughly 3000 citations? (Probably many repeats so the number would be less.)
posted by grouse at 10:03 PM on October 30, 2012

If the "paywall" is an EzProxy server using the "get it" service, you can probably set Mendeley up to allow you to go directly to the journal's or content provider's page for each article (though not directly to the PDF, that will usually be one more click) from within Mendeley. This will be most useful if you have already imported all of her citations, which I assume you have. If this is the situation, there will probably be instructions available from your library: google "mendeley ezproxy [your institution]". Here's an example.

As for the references, it is possible to export them with the document citation, but I'm fairly sure you'll have to use Scopus--I don't think PubMed includes them in its abstract data.

In Scopus, click the "export" link (it has a little green document icon with an arrow protruding from its right side) either after checking/selecting multiple documents from your search results or from a single article's abstract page. The "Abstract format with References" and "Complete" options will include the cited works from your article(s) in the citation. They will probably all be piled into a single field, and separated by semicolons or something. As far as importing these data into Mendeley, though, you're on your own.

Good luck!
posted by pullayup at 10:33 PM on October 30, 2012

Alternately, Scopus will allow you to select references from the list of citations within an article's abstract page, and export them as discrete references (rather than piled into a single field), if that makes sense. There's a second "export" link at the top of the citation list, below the abstract proper.

If you do this, you 1) will need to export each of her papers' references separately, and 2) would be giving each citation an independent existence within Mendeley (the "roughly 3000 citations" grouse mentioned), rather than confining them to a (custom?) field within the citation for the paper which cited them.

I hope this made sense, and I apologize for my ignorance of Mendeley. Feel free to drop me a line if you need clarification.
posted by pullayup at 10:41 PM on October 30, 2012

Web of Science will allow you to select multiple articles and download them in various formats. I know that for Endnote you can do this, I assume there is a format for Mandeley too, although I don't know that program well.
posted by fshgrl at 10:46 PM on October 30, 2012 [1 favorite]

To clarify, Web of Science allows you to download all of the saved articles at once as an export in the format you need: that would be the time savings. You check all the ones you want then go to export and specify the format and it does it in on operation.
posted by fshgrl at 10:48 PM on October 30, 2012

I don't know the answer to your question, but if I were in your shoes I would contact my school librarian who would. Your school might not have as helpful of a librarian as mine but it might be worth a try.
posted by pwb503 at 1:01 PM on October 31, 2012 [1 favorite]

Your question implies that your PI doesn't have a PDF copy of all her articles, which seems a bit strange to me, but if that's indeed the case, grouse's method might be the most effective.

You could also try searching Mendeley's catalog using author:Bob Smith to limit your search. You'll probably need to limit it by field and maybe keyword too, but if you can find a page for the entries already in Mendeley's catalog, you can add them directly from there, and if you've entered your library's details in your import settings, you can have the PDF added directly. Definitely ask your librarian about this, but be sure to emphasize that you want the PDFs, not just the metadata.

Ideally you could just get an export from Pubmed and add it directly, but that doesn't quite work yet. Once everything is published open access, this will be easier.

Don't forget to add her publications to her profile, too. Here's mine.

You'll have to use a service like Scopus right now to get cited papers, but Mendeley is working on extracting references for you. Some papers have a references tab, but not all do, and there's not currently a good way to import these, but that feature is coming.
(I work at Mendeley)
posted by Mr. Gunn at 8:58 PM on November 4, 2012