"Armin Goralczyk" <[EMAIL PROTECTED]> wrote in
news:[EMAIL PROTECTED]:
> On Dec 15, 2007 6:31 PM, David Winsemius <[EMAIL PROTECTED]>
> wrote:
>> > pm.srch<- function (){
>> srch.stem
>> <-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pub
>> med&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"
snipped list of IDs
>>
>>
> 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&ter
> m=laryngeal neoplasms[mh]
> I/O warning : failed to load external entity
> "http%3A//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi%3Fdb=pubme
> d&term=laryngeal%20neoplasms%5Bmh%5D"
>>
> What's wrong?
I'm not sure. You included my simple example. rather than your search string
that provoked an error. This is an example search that one can find on
the how-to page for literature searches with /esearch:
http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=PNAS[ta]+AND+97[vi]&retstart=6&retmax=6&tool=biomed3
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.
When I use the search terms in NCBI's example I get:
> 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)
+ }
> doc.xml<-pm.srch()
1: "PNAS[ta]+AND+97[vi]"
2:
Read 1 item
> doc.xml
//Id
[1,] "16578858"
[2,] "11186225"
[3,] "11121081"
[4,] "11121080"
[5,] "11121079"
[6,] "11121078"
[7,] "11121077"
[8,] "11121076"
[9,] "11121075"
[10,] "11121074"
[11,] "11121073"
[12,] "11121072"
[13,] "11121071"
[14,] "11121070"
[15,] "11121069"
[16,] "11121068"
[17,] "11121067"
[18,] "11121066"
[19,] "11121065"
[20,] "11121064"
--
David Winsemius, MD
> Thanks for any help
> --
> Armin Goralczyk, M.D.
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