PubMed2XL 1.0 available

I've uploaded a new version of PubMed2XL, a Windows application that converts article lists from PubMed.gov into Microsoft Excel files.

Unlike downloading the CSV directly from PubMed.gov, PubMed2XL gives users (OK … advanced users) the ability to customize the output but even the default format includes Abstract, links to each article, and even links to related articles, and reviews.

Here's an example of a spreadsheet made with PubMed2XL and here's the source file used to make it. The source file was downloaded from PubMed.gov using a search for "Mexican flu".

If you'd like to use the software you can download it for free.

If you notice any bugs or have any questions or remarks, please feel free to leave a comment on the site. Thanks!

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2 Comments

  1. Jeevan

    Hi Nitin, 
    Great job! i have used the tool few times and it works absolutely fine. a quick question, it doesn't seems to work with pubmed central files. is there any other way i can convert pubmed central xml files to excel?
    Thanks,
    Jeevan

    Reply
    1. nitin (Post author)

      Hi Jeevan,

      I think the PubMed Central files are completely different on the inside, so PubMed2XL can't parse those as it's only been designed to "know" about the PubMed XML format.

      The same techniques could be used to do PubMed Central files as well. Excel does let you import XML files but the results could be very messy and require a lot of cleanup. Having said that, I'd recommend trying that first.

      Let me know what you're trying to do exactly; I might have some suggestions.

      Thanks,
      Nitin

      Reply

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