Analyzing Publications from Pubmed via XML
On Dec 13, 2007 9:03 PM, Farrel Buchinsky <fjbuch at gmail.com> 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.
Has anyone ever done this and could you share your script? Are there any
published examples where the end result is a dataframe.
I guess what I am looking for is an easy and simple way to parse the feed
and extract the data. Alternatively how does one turn an RSS feed into a CSV
file?
Try this:
library(XML)
doc <-
xmlTreeParse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-",
isURL = TRUE, useInternalNodes = TRUE)
sapply(c("//author", "//category"), xpathApply, doc = doc, fun = xmlValue)