or just try looking in the annotate package from Bioconductor
Gabor Grothendieck wrote: > On Dec 13, 2007 9:03 PM, Farrel Buchinsky <[EMAIL PROTECTED]> 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) > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.