Download PubMed Search Results Into a Spreadsheet with FLink

Hat tip to Patricia at the Dragonfly blog for her pointer to FLink, (Frequency-weighted Links), a tool for downloading PubMed results into a CSV file (suitable for opening in Excel or OpenOffice.) You can access FLink at http://www.ncbi.nlm.nih.gov/Structure/flink/flink.cgi.

You can use Patricia’s post for step-by-step directions for using FLink, but it’s pretty easy. Use the pulldown menu to specify the database you want to search (there are a few available besides PubMed.) Then from the popup window choose “Search Entrez” and enter your search keywords. FLink will think about it a minute and show your search results in the browser window. (I searched for autism and got 16502 results.)

From there, click “Download CSV.” In the case of the autism search I did, it took several minutes for FLink to assemble a CSV for me — but once it did, it was a 5MB download that listed over 16300 articles from PubMed, including PubMed ID, Authors, Title, Month and Year of publication, and Summary.

Now if direct links to the articles were included you could jimmy up a little Perl and have a nice download utility, but unfortunately links are not available. However just to be weird I took the last thousand article titles in the downloaded CSV (I wanted to do more but Wordle got stroppy) and made a tag cloud of the top 75 words.

A nice tool. I feel guilty for wishing there were more data downloaded with the CSV.

About researchbuzz

Covering the world of search engines, databases, and other online information collections since 1996.

Posted on November 22, 2010, in Uncategorized and tagged , , . Bookmark the permalink. 1 Comment.

  1. If you’re working with CSV or anything similar, you should try Refine.

    http://code.google.com/p/google-refine/

    It changes lives.

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