[R] Analyzing Publications from Pubmed via XML

[Armin Goralczyk]

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.
--
Universitätsmedizin Göttingen
Abteilung Allgemein- und Viszeralchirurgie
Rudolf-Koch-Str. 40
39099 Göttingen
--
Dept. of General Surgery
University of Göttingen
Göttingen, Germany
--
http://www.chirurgie-goettingen.de