Message-ID: <AC9C43A9-C918-42D7-A397-FC77E43AC3BC@indiana.edu>
Date: 2007-12-14T02:12:43Z
From: Rajarshi Guha
Subject: Analyzing Publications from Pubmed via XML
In-Reply-To: <bd93cdad0712131803t22eed96bk9fd2010b3aa745a9@mail.gmail.com>
On Dec 13, 2007, at 9:03 PM, Farrel Buchinsky wrote:
> I would like to track in which journals articles about a particular
> disease
> are being published. Creating a pubmed search is trivial. The search
> provides data but obviously not as an R dataframe. I can get the
> search to
> export the data as an xml feed and the xml package seems to be able
> to read
> it.
>
> xmlTreeParse("
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?
> rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-
> ",isURL=TRUE)
>
> But getting from there to a dataframe in which one column would be
> the name
> of the journal and another column would be the year (to keep things
> simple)
> seems to be beyond my capabilities.
If you're comfortable with Python (or Perl, Ruby etc), it'd be easier
to just extract the required stuff from the raw feed - using
ElementTree in Python makes this a trivial task
Once you have the raw data you can read it into R
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Rajarshi Guha <rguha at indiana.edu>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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A committee is a group that keeps the minutes and loses hours.
-- Milton Berle