6.183
Extract and Transform PubMed XML Data using XSLT

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## Loading required package: xml2

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Introduction

Apply Transformation

library(xml2)
library(xslt)

xslFn <- "xsl/PubMed2PMSubset.xsl"

xmlfolder <- "pubmed-xml" 
tfmfolder <- "pubmed-xml-tfm"

xmlfiles <- list.files(path = xmlfolder, pattern = ".xml$", full.names = T)
numXMLFiles <- length(xmlfiles)

for (i in 1:numXMLFiles) {
  # apply transform to each file
  xmlDoc <- read_xml(xmlfiles[i])
  xslStyle <- read_xml(xslFn)

  transformedXML <- xml_xslt(xmlDoc, xslStyle)

  xmlFnBase <- basename(xmlfiles[i])
  
  txnFn <- paste0(tfmfolder,'/',
                  substring(xmlFnBase, 1, nchar(xmlFnBase)-4),
                  '-tf.xml')
  
  status <- write_xml(transformedXML, file = txnFn)
}

xmlDoc <- xmlParse("pubmed-xml-tfm/pubmed22n0007-tf.xml")

root <- xmlRoot(xmlDoc)

length(xmlChildren(root))

## [1] 30000

journals = xpathApply(xmlDoc, "//Journal/Title", xmlValue)

Conclusion

This tutorial provided an example on how to extract data from an XML file into a new XML file with a different structure using XSLT.

Tutorial

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