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Editorial Team
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Asked: 2026-06-12T06:54:35+00:00

I wish to get a XML file produced by EndNote into an R data

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I wish to get a XML file produced by EndNote into an R data frame.

I would like each final child node (e.g. title, author…) to be a column

An example EndNote xml file is available here:

Example on gist

I have yet to resolve this using library(XML). I am hoping someone has a ready made solution, sorry if this sounds lazy.

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1 Answer

  1. Editorial Team

    I had a similar problem to convert to a dataframe. I used xmlToDataFrame on the child nodes.

    library(XML)
library(RCurl)
urldata<-"https://gist.github.com/raw/3831049/80f1315ba03d278b4f5f0d916fb1999709fc40e6/endnote.xml"
urldata<-xmlParse(getURL(urldata,ssl.verifypeer = FALSE,.opts=curlOptions(followlocation=TRUE)))
xmlToDataFrame(getNodeSet(urldata,'//*/record'))

#             database source-app rec-number foreign-keys ref-type
# 1 EndNote Ecology.enl    EndNote      13264        13264       17
# 2 EndNote Ecology.enl    EndNote      13265        13265       17
#        contributors                                  auth-address
# 1    Chapman, A. G. Cent States Forest Expt Stn, Columbus, OH USA
# 2 Strohecker, H. F.                 Univ Chicago, Chicago, IL USA
#                                                                                                     titles
# 1 An ecological basis for reforestation of submariginal lands in the Central Hardwood RegionEcologyEcology
# 2                                          A survey of soil temperatures in the Chicago areaEcologyEcology
#       periodical alt-periodical   pages volume number   dates      isbn
# 1 EcologyEcology EcologyEcology  93-105     18      1 1937Jan 0012-9658
# 2 EcologyEcology EcologyEcology 162-168     18      1 1937Jan 0012-9658
#         accession-num                                           notes
# 1 ISI:000200148800007  V02fg\rTimes Cited:5\rCited References Count:2
# 2 ISI:000200148800014 V02fg\rTimes Cited:5\rCited References Count:14
#                            urls language
# 1 <Go to ISI>://000200148800007  English
# 2 <Go to ISI>://000200148800014  English

    There maybe some problems with multiple authors (doesnt occur here) etc if used in general which would require probably a slight change.

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