[R] Analyzing Publications from Pubmed via XML

[Rajarshi Guha]

On Dec 13, 2007, at 9:16 PM, Farrel Buchinsky wrote:

> I am afraid not! The only thing I know about Python (or Perl, Ruby  
> etc) is that they exist and that I have been able to download some  
> amazing freeware or open source software thanks to their existence.
> The XML package and specifically the xmlTreeParse function looks as  
> if it is begging to do the task for me. Is that not true?


Certainly - probably as a better Python programmer than an R  
programmer, it's faster and neater for me to do it in Python:

from elementtree.ElementTree import XML
import urllib

url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi? 
rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-'
con = urllib.urlopen(url)
dat = con.read()
root = XML(dat)
items = root.findall("channel/item")
for item in items:
     category = item.find("category")
     print category.text

The problem is that the RSS feed you linked to, does not contain the  
year of the article in an easily accessible XML element. Rather you  
have to process the HTML content of the description element - which,  
is something R could do, but you'd be using the wrong tool for the job.

In general, if you're planning to analyze article data from Pubmed  
I'd suggest going through the Entrez CGI's (ESearch and EFetch)   
which will give you all the details of the articles in an XML format  
which can then be easily parsed in your language of choice.

This is something that can be done in R (the rpubchem package  
contains functions to process XML files from Pubchem, which might  
provide some pointers)

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Rajarshi Guha  <rguha at indiana.edu>
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Writing software is more fun than working.