Re: [R] Analyzing Publications from Pubmed via XML

From: Duncan Temple Lang <>
Date: Sat, 15 Dec 2007 11:07:21 +1300

Hash: SHA1

Farrel Buchinsky wrote:

>> 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.

> Yes. I have noticed that there two sorts of xml that pubmed will
> provide. The kind I had hooked into was an rss feed which provides a
> lot of the information simply as a formatted table for viewing in a
> rss reader. There is another way to get the xml to come out with more
> tags. However, I found the best way to do this is probably through the
> bioconductor annotate package
> x <- pubmed("18046565", "17978930", "17975511")
> a <- xmlRoot(x)
> numAbst <- length(xmlChildren(a))
> absts <- list()
> for (i in 1:numAbst) {
> absts[[i]] <- buildPubMedAbst(a[[i]])
> }

You can simplify the final 5 lines to

   absts = xmlApply(a, buildPubMedAbst)

which is shorter, fractionally faster and handles cases where there are no abstracts.

> I am now trying to work through that approach to see what I can come up with.
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