and yet more PubMed to Excel news

I've updated the documentation for PubMed2XL, a Windows application that converts article lists from pubmed.gov into Microsoft Excel files. The documentation isn't incredibly thorough, but I think it's enough to work for now.

Speaking of getting PubMed search results into a spreadsheet check this out:

Those who search PubMed regularly have often wished for a way to import search results into a a program such as Excel. It’s here! A new tool called FLink (Frequency-weighted Links) is now accessible from the NIH National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/Structure/flink/docs/flink_about.html. FLink allows PubMed search results to be saved as a CSV, or comma-separated value, file which can be imported into a program like Excel.

source: Dragonfly » Blog Archive » FLink: A New Way to Save PubMed Search Results. Retrieved November 13, 2010, from http://nnlm.gov/pnr/dragonfly/2010/11/10/flink-a-new-way-to-save-pubmed-search-results/

For instructions, just click here.

Unfortunately, those instructions don't instruct the user to to import the CSV file with UTF-8 encoding, etc. Not using the correct character encoding upon import could cause characters like accents and umlauts that might appear in author names, for example, to appear as strange, nonsensical characters.

Also, the output format is fixed – i.e. I don't think the user has any control of what data gets exported to the CSV file. Some data is concatenated together in one spreadsheet cell and that can be a problem for those who need to parse the data at a more granular level. It's more difficult to split data and re-sort it than it is to concatenate data that is already parsed in a granular fashion.

On the contrary, the PubMed2XL output can be customized – although it requires some skill with XML. Also, it places in each cell only one value and lastly I've never experienced any character encoding issues in the tests I've done.

Sure, I'm trying to compare the two approaches – just a touch, but in the end the best way will be for the users to have an easy interface offered directly from PubMed.gov and its related sites. I'm just saying that I hope they soon offer more options and a more user-friendly method for the sake of the user.

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2 Comments

  1. Jagdish

    I am an average computer friendly librarian working for academic work based on PubMed. I wish to know how to extract citations based on Affiliation with PubMed2XL.
    thanks

    Reply
    1. nitin (Post author)

      Hi Jagdish,

      Thanks for your question.

      If you want to add an "affiliation" column to the PubMed2XL output please see this comment:
      http://blog.humaneguitarist.org/projects/pubmed2xl/#comment-213

      If you want to actually retrieve search results based on affiliation, I think you'll probably need to use PubMed.gov's Advanced Search (http://www.ncbi.nlm.nih.gov/pubmed/advanced) and probably use the "Author – Corporate" field to narrow your results.

      thanks,
      Nitin

      Reply

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