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Using Perl to Query PubMed

by Anonymous Monk
on Oct 11, 2013 at 03:36 UTC ( #1057810=perlquestion: print w/replies, xml ) Need Help??

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

I'm totally new to Perl and wondered if you could help me understand if/how I can use it to do this:

Query PubMed/MEDLINE for all articles that contain, in the body of the text/pdf, mutations related to disease Y. Then download the links to the articles.

Is this possible?

Replies are listed 'Best First'.
Re: Using Perl to Query PubMed
by kcott (Archbishop) on Oct 11, 2013 at 03:58 UTC

    That sort of thing is certainly possible. I don't know what "PubMed/MEDLINE" is, so I can't give a definite "yes" in this particular instance. I wrote something last year, which seems to be quite close to what your after: Re: Download references list in pdf format with script. At least, that may give you a starting point.

    -- Ken

Re: Using Perl to Query PubMed
by Old_Gray_Bear (Bishop) on Oct 11, 2013 at 08:02 UTC
    A quick search of CPAN turned up Boulder::Medline (written by Lincoln Stein in 2007) and a whole raft of Bio::Biblio::MedlineXXXX modules from Carne Draug dated this year. You might explore your options there.

    Nota Bene: I am not a wet-sciences guy. The last Biology course I took was at least fourty years ago.

    I Go Back to Sleep, Now.


Re: Using Perl to Query PubMed
by derby (Abbot) on Oct 11, 2013 at 12:59 UTC

    The folks at NCBI (part of NIH) have a web api called entrez that you can use to search then fetch pubmed articles (among numerous other NIH databases).


    Update ... should have mentioned, a lot of their examples are in perl

      Definitely use entrez tools, no need to re-do this on your own.
      Another good tool, also Perl-based, is PubCrawler. It "goes to the library, while you go to the pub."

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