Message-ID: <a695fbee0712170618t74888388sc303646454ee65db@mail.gmail.com>
Date: 2007-12-17T14:18:03Z
From: Armin Goralczyk
Subject: Analyzing Publications from Pubmed via XML
In-Reply-To: <Xns9A077F740B4A0dNOTwinscomcast@80.91.229.13>
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