Creating a dataset from an XML file in R statistics - r

Question

I am trying to download an XML file of journal article records and create a dataset for further interrogation in R. I'm completely new to XML and quite novice at R. I cobbled together some code using bits of code from 2 sources:
GoogleScholarXScraper
and
Extracting records from pubMed
library(RCurl)
library(XML)
library(stringr)
#Search terms
SearchString<-"cancer+small+cell+non+lung+survival+plastic"
mySearch<-str_c("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",SearchString,"&usehistory=y",sep="",collapse=NULL)
#Seach
pub.esearch<-getURL(mySearch)
#Extract QueryKey and WebEnv
pub.esearch<-xmlTreeParse(pub.esearch,asText=TRUE)
key<-as.numeric(xmlValue(pub.esearch[["doc"]][["eSearchResult"]][["QueryKey"]]))
env<-xmlValue(pub.esearch[["doc"]][["eSearchResult"]][["WebEnv"]])
#Fetch Records
myFetch<-str_c("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=",env,"&retmode=xml&query_key=",key)
pub.efetch<-getURL(myFetch)
myxml<-xmlTreeParse(pub.efetch,asText=TRUE,useInternalNodes=TRUE)
#Create dataset of article characteristics #This doesn't work
pub.data<-NULL
pub.data<-data.frame(
journal <- xpathSApply(myxml,"//PubmedArticle/MedlineCitation/MedlineJournalInfo/MedlineTA", xmlValue),
abstract<- xpathSApply(myxml,"//PubmedArticle/MedlineCitation/Article/Abstract/AbstractText",xmlValue),
affiliation<-xpathSApply(myxml,"//PubmedArticle/MedlineCitation/Article/Affiliation", xmlValue),
year<-xpathSApply(myxml,"//PubmedArticle/MedlineCitation/Article/Journal/JournalIssue/PubDate/Year", xmlValue)
,stringsAsFactors=FALSE)
The main problem I seem to have is that my returned XML file is not completely uniformly structured. For example, some references have a node structure like this:
- <Abstract>
<AbstractText>The Wilms' tumor gene... </AbstractText>
Whilst some have labels and are like this
- <Abstract>
<AbstractText Label="BACKGROUND & AIMS" NlmCategory="OBJECTIVE">Some background text.</AbstractText>
<AbstractText Label="METHODS" NlmCategory="METHODS"> Some text on methods.</AbstractText>
When I extract the 'AbstactText' I am hoping to get 24 rows of data back (there are 24 records when I run this made up search today), but xpathSApply returns all labels within 'AbstactText' as individual elements of my dataframe. Is there a way to collapse the XML structure in this instance/Ignore the labels? Is there a way to make xpathSApply return 'NA' when nothing is found at end of a path? I am aware of xmlToDataFrame, which sounds like it should fit the bill, but whenever I try to use this it doesn't seem to give me anything sensible.
Thanks for your help

Answer 1

I am unsure as to which you want however:
xpathSApply(myxml,"//*/AbstractText[#Label]")
will get the nodes with labels (keeping all attributes etc).
xpathSApply(myxml,"//*/AbstractText[not(#Label)]",xmlValue)
will get the nodes without labels.
EDIT:
test<-xpathApply(myxml,"//*/Abstract",xmlValue)
> length(test)
[1] 24
may give you what you want
EDIT:
to get affiliation, year etc padded with NA's
dumfun<-function(x,xstr){
res<-xpathSApply(x,xstr,xmlValue)
if(length(res)==0){
out<-NA
}else{
out<-res
}
out
}
xpathSApply(myxml,"//*/Article",dumfun,xstr='./Affiliation')
xpathSApply(myxml,"//*/Article",dumfun,xstr='./Journal/JournalIssue/PubDate/Year')