Analyzing Publications from Pubmed via XML
On Dec 15, 2007 6:31 PM, David Winsemius <dwinsemius at comcast.net> wrote:
After quite a bit of hacking (in the sense of ineffective chopping with
a dull ax), I finally came up with:
pm.srch<- function (){
srch.stem<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term="
query<-readLines(con=file.choose())
query<-gsub("\\\"","",x=query)
doc<-xmlTreeParse(paste(srch.stem,query,sep=""),isURL = TRUE,
useInternalNodes = TRUE)
return(sapply(c("//Id"), xpathApply, doc = doc, fun = xmlValue) )
}
pm.srch() #choosing the search-file
//Id
[1,] "18046565"
[2,] "17978930"
[3,] "17975511"
[4,] "17935912"
[5,] "17851940"
[6,] "17765779"
[7,] "17688640"
[8,] "17638782"
[9,] "17627059"
[10,] "17599582"
[11,] "17589729"
[12,] "17585283"
[13,] "17568846"
[14,] "17560665"
[15,] "17547971"
[16,] "17428551"
[17,] "17419899"
[18,] "17419519"
[19,] "17385606"
[20,] "17366752"
I tried the example above, but only the first 20 PMIDs will be returned. How can I circumvent this (I guesss its a restraint from pubmed)?
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