Beefy Boxes and Bandwidth Generously Provided by pair Networks
The stupid question is the question not asked

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 (Bishop) 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."

Log In?

What's my password?
Create A New User
Domain Nodelet?
Node Status?
node history
Node Type: perlquestion [id://1057810]
Approved by kcott
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others romping around the Monastery: (3)
As of 2022-05-24 16:42 GMT
Find Nodes?
    Voting Booth?
    Do you prefer to work remotely?

    Results (84 votes). Check out past polls.