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Tool to download all PDFs associated with results to a pubmed query?

Is there a tool that will download all PDFs given a query to Pubmed or PMC?

Could work by pulling only articles found in PMC, but ideally would grab any article to which a link not behind a paywall is found.

Thank you!

eutils ncbi pubmed entrez
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updated by jena • jena • written by LauferVA LauferVA

2 answers

Writing a wrapper for https://github.com/billgreenwald/Pubmed-Batch-Download gave me the results I needed.

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written by LauferVA LauferVA

Zotero should be able to do that, maybe also Mendeley or other citation managers. I recall it was possible with results on Google scholar. You may need to visit multiple results pages to grab all papers.

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written by jena • jena

point of this post is to have a command line tool that automates the process. See, for instance, https://github.com/billgreenwald/Pubmed-Batch-Download though I found this unwieldly. In the interim since writing this post I wrote a little python wrapper for that package and it runs smoothly now.

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written by LauferVA LauferVA

Fair enough. Perhaps others prefer point-and-click method, so my answer can still be of use to some.

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written by jena • jena

in that case please consider writing your own post where a point and click answer is the subject of the post, then answering it with the text you have above.

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written by LauferVA LauferVA

I see nowhere in the post a mention that a CLI tool is required. Also, I'm not really comfortable asking questions that other people asked. I think the answer can stay here just fine.

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written by jena • jena

i suppose ill also add that a careful reading of the phrasing of my post would have obviated the need for reference to something like zotero. still, thanks for trying.

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written by LauferVA LauferVA

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