Re: [R] Extract just some fields from XML

From: Sean Davis <sdavis2_at_mail.nih.gov>
Date: Mon 09 May 2005 - 10:38:41 EST

Gregor,

I'm not answering your question directly, but have you looked at the bioconductor package "annotate"? I bet it does much of what you are trying to do....

http://www.bioconductor.org/repository/release1.5/package/html/index.html

List of functions:

http://www.bioconductor.org/repository/release1.5/package/html/descrips/annotateDesc.html

Sean

> Hello!
>
> I am trying to get specific fields from an XML document and I am totally
> puzzled. I hope someone can help me.
>
> # URL
> URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation"
> # download a XML file
> tmp <- xmlTreeParse(URL, isURL = TRUE)
> tmp <- xmlRoot(tmp)
>
> Now I want to extract only node 'pubdate' and its children, but I don't
> know how to do that unless I try to dig into the structure of the XML
> file. The problem is that structure can differ and then hardcoded set
> of list indices i.e. tmp[[i]][[j]]... doesn't help me.
>
> I've read xmlEventParse but I don't understand handlers part up to the
> point that I could get anything usable from it. Here is something not
> very usable ;)
>
> PubDate <- function(x, ...)
> {
> print(x)
> }
> xmlEventParse(URL, isURL = TRUE,
> handlers=list(PubDate=PubDate),
> addContext = FALSE)
>
> Thanks in advance!
>
> Lep pozdrav / With regards,
> Gregor Gorjanc
>
> ----------------------------------------------------------------------
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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon May 09 10:46:49 2005

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