Analyzing Publications from Pubmed via XML
On Dec 15, 2007 6:31 PM, David Winsemius <dwinsemius at comcast.net> wrote:
pm.srch<- function (){
srch.stem <-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=" query <-as.character(scan(file="",what="character")) doc <-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE, useInternalNodes = TRUE) sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue) }
pm.srch()
1: "laryngeal neoplasms[mh]"
2:
Read 1 item
//Id
[1,] "18042931"
[2,] "18038886"
[3,] "17978930"
[4,] "17974987"
[5,] "17972507"
[6,] "17970149"
[7,] "17967299"
[8,] "17962724"
[9,] "17954109"
[10,] "17942038"
[11,] "17940076"
[12,] "17848290"
[13,] "17848288"
[14,] "17848287"
[15,] "17848278"
[16,] "17938330"
[17,] "17938329"
[18,] "17918311"
[19,] "17910347"
[20,] "17908862"
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:
Read 1 item
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"
What's wrong? Thanks for any help
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