Question

How To Download A Few Hundred Pdfs From Pubmed

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12.5 years ago

sebrowns ▴ 80

What is the best way to download PDFs from PubMed programmatically. For example, given a PubMed URL:

http://www.ncbi.nlm.nih.gov/pubmed/9016068

Whats the best way to obtain the PDF of the paper? I've tried to use NCBI eutils and other things, but can't seem to find a solution. Thanks for your time.

pubmed • 37k views

ADD COMMENT • link updated 12.5 years ago by Pierre Lindenbaum 164k • written 12.5 years ago by sebrowns ▴ 80

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see if this similar question can help you: http://www.biostars.org/post/show/2928/taverna-workflow-to-retrieve-1500-papers-for-one-or-two-keywords-as-plain-text/

ADD REPLY • link 12.5 years ago by Giovanni M Dall'Olio 28k

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I'm using PaperFetch from http://www.papertoolbox.com and it's really cool.

ADD REPLY • link 12.4 years ago by AyazN ▴ 10

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For anyone still looking into this, I updated the program to work with the current version of ruby in 2015 (version 2.1.2).

https://github.com/billgreenwald/Pubmed-Batch-Download

ADD REPLY • link 9.2 years ago by billgreenwald ▴ 20

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I forked your repo bill and packaged it so it is easier to run in python https://github.com/ddomingof/PubMed2PDF

ADD REPLY • link 5.4 years ago by ddomingof • 0

score 8 · Answer 1 · 2012-05-24

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12.5 years ago

Pierre Lindenbaum 164k

See the PubmedPDF : https://github.com/elfar/PubmedPDF

This program tries to download a PDF file for the given comma-separated pubmed IDs

ADD COMMENT • link 12.5 years ago by Pierre Lindenbaum 164k

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For anyone still looking into this, I updated the program to work with the current version of ruby in 2015 (version 2.1.2).

https://github.com/billgreenwald/Pubmed-Batch-Download

ADD REPLY • link 9.2 years ago by billgreenwald ▴ 20

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Hello, I can confirm that it Bill's update works in Windows 10 with Ruby 2.2.0. To get it to run in Windows via the Windows cmd command line you need to put quotes around the list of PMIDs

ADD REPLY • link 8.3 years ago by david.mcallister ▴ 10

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any idea how do you convert doi to pubmed id?

ADD REPLY • link 12.4 years ago by Hranjeev ★ 1.5k

score 0 · Answer 2 · 2012-05-24

I found this post online: http://bioinformatics.risha.me/tag/eutils/

I have used eutils a lot but have never used it to get pdf version of any paper. First of all, I don't think PMC or Pubmed Central has access to the full articles for all the PMID's. I think for most of the times they only give you title and abstract information. Second thing is that you can download the xml files containing full text for the articles (in case the full text is available) present in PMC but I don't think you can get a pdf for the articles.