[R] Analyzing Publications from Pubmed via XML

[David Winsemius]

On 15 Dec 2007, you wrote in gmane.comp.lang.r.general:

> If we can assume that the abstract is always the 4th paragraph then we
> can try something like this:
> 
> library(XML)
> doc <-
> xmlTreeParse("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss
> _guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-", isURL = TRUE,
> useInternalNodes = TRUE, trim = TRUE) 
> 
> out <- cbind(
>      Author = unlist(xpathApply(doc, "//author", xmlValue)),
>      PMID = gsub(".*:", "", unlist(xpathApply(doc, "//guid",
>      xmlValue))), 
>      Abstract = unlist(xpathApply(doc, "//description",
>           function(x) {
>                on.exit(free(doc2))
>                doc2 <- htmlTreeParse(xmlValue(x)[[1]], asText = TRUE,
>                     useInternalNodes = TRUE, trim = TRUE)
>                xpathApply(doc2, "//p[4]", xmlValue)
>           }
>      )))
> free(doc)
> substring(out, 1, 25) # display first 25 chars of each field
> 
> 
> The last line produces (it may look messed up in this email):
> 
>> substring(out, 1, 25) # display it
>       Author                      PMID       Abstract
 [1,] " Goon P, Sonnex C, Jani P" "18046565" "Human papillomaviruses (H"
 [2,] " Rad MH, Alizadeh E, Ilkh" "17978930" "Recurrent laryngeal papil"
 [3,] " Lee LA, Cheng AJ, Fang T" "17975511" "OBJECTIVES:: Papillomas o"
 [4,] " Gerein V, Schmandt S, Ba" "17935912" "BACKGROUND: Human papillo"
snip
> 
> 

It looked beautifully regular in my newsreader. It is helpful to see an 
example showing the indexed access to nodes. It was also helpful to see the 
example of substring for column display. Thank you (for this and all of 
your other contributions.)

I find upon further browsing that the pmfetch access point is obsolete. 
Experimentation with the PubMed eFetch server access point results in fully 
xml-tagged results:

e.fetch.doc<- function (){
   fetch.stem <-
        "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
   src.mode <- "db=pubmed&retmode=xml&"
   request <- "id=11045395"
   doc<-xmlTreeParse(paste(fetch.stem,src.mode,request,sep=""),
                          isURL = TRUE, useInternalNodes = TRUE)
     }
# in the debugging phase I needed to set useInternalNodes = TRUE to see the  
tags. Never did find a way to "print" them when internal.

doc<-e.fetch.doc()
get.info<- function(doc){
         df<-cbind(
 	Abstract = unlist(xpathApply(doc, "//AbstractText", xmlValue)),
 	Journal =  unlist(xpathApply(doc, "//Title", xmlValue)),
 	Pmid =  unlist(xpathApply(doc, "//PMID", xmlValue))
                   )
   return(df)
   } 

# this works
> substring(get.info(doc), 1, 25)
     Abstract                    Journal                     Pmid      
[1,] "We studied the prevalence" "Pediatric nephrology (Ber" "11045395"


-- 
David Winsemius