Analyzing Publications from Pubmed via XML
On 12/18/07, David Winsemius <dwinsemius at comcast.net> wrote:
David Winsemius <dwinsemius at comcast.net> wrote in news:Xns9A09CA51DB1E4dNOTwinscomcast at 80.91.229.13:
"Armin Goralczyk" <agoralczyk at gmail.com> wrote in news:a695fbee0712171238g4995040x579e58f52f83376e at mail.gmail.com:
I tried the above function with simple search terms and it worked fine for me (also more output thanks to Martin's post) but when I use search terms attributed to certain fields, i.e. with [au] or [ta], I get the following error message:
pm.srch()
1: "laryngeal neoplasms[mh]" 2:
I am wondering if you used spaces, rather than "+"'s? If so then you may want your function to do more gsub-processing of the input string.
I tried my theory that one would need "+"'s instead of spaces, but disproved it. Spaces in the input string seems to produce acceptable results on my WinXP/R.2.6.1/RGui system even with more complex search strings. --
It's not the spaces, the problem is the tag (sorry that I didn't
specify this), or maybe the string []. I am working on a Mac OS X 10.4
with R version 2.6. Is it maybe a string conversion problem? In the
following warning strings in the html adress seem to be different:
Fehler in .Call("RS_XML_ParseTree", as.character(file), handlers,
as.logical(ignoreBlanks), :
error in creating parser for
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=laryngeal
neoplasms[mh]
I/O warning : failed to load external entity
"http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubmed&term=laryngeal%20neoplasms%5Bmh%5D"
Armin Goralczyk, M.D. -- Universit?tsmedizin G?ttingen Abteilung Allgemein- und Viszeralchirurgie Rudolf-Koch-Str. 40 39099 G?ttingen -- Dept. of General Surgery University of G?ttingen G?ttingen, Germany -- http://www.chirurgie-goettingen.de