rxmlxpathpubmedropensci

Parsing XML file in R using rentrez

I am not an XML expert. I am having an issue when parsing XML file using rentrez. I am trying to have author and affiliation by each pmid (article id in PubMed database) as an output. I have code that works well except when author has multiple affiliations. When author have multiple affiliations the length of columns first_names, last_names, and affiliation become different and it returns an error. I really do not have expertise in xml parsing to handle that. I am strictly expecting a result like below: 

pmid         first_names  last_names              affiliation
27869504     Luca           Villa         Division of Experimental Oncology/Unit of Urology, URI , IRCCS Ospedale San Raffaele, Milan, Italy 
27869504     Luca           Villa         Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France
27869504     Tarik Emre     Şener         Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France
27869504     Tarik Emre     Şener         Department of Urology, Marmara University School of Medicine, Istanbul, Turkey

Structure of my sample XML file returned by entrez_fetch is below:

 <?xml version="1.0"?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2017//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd">
<PubmedArticleSet>
  <PubmedArticle>
   <MedlineCitation Status="In-Data-Review" Owner="NLM">
    <PMID Version="1">27869504</PMID>
    <DateCreated>
     <Year>2016</Year>
     <Month>11</Month>
      <Day>21</Day>
    </DateCreated>
  <DateRevised>
    <Year>2017</Year>
    <Month>01</Month>
    <Day>06</Day>
  </DateRevised>
  <Article PubModel="Print-Electronic">
    <Journal>
      <ISSN IssnType="Electronic">1557-900X</ISSN>
      <JournalIssue CitedMedium="Internet">
        <Volume>31</Volume>
        <Issue>1</Issue>
        <PubDate>
          <Year>2017</Year>
          <Month>Jan</Month>
        </PubDate>
      </JournalIssue>
      <Title>Journal of endourology</Title>
      <ISOAbbreviation>J. Endourol.</ISOAbbreviation>
    </Journal>
    <ArticleTitle>Initial Content Validation Results of a New Simulation Model for Flexible Ureteroscopy: The Key-Box.</ArticleTitle>
    <Pagination>
      <MedlinePgn>72-77</MedlinePgn>
    </Pagination>
    <ELocationID EIdType="doi" ValidYN="Y">10.1089/end.2016.0677</ELocationID>
    <Abstract>
      <AbstractText Label="PURPOSE" NlmCategory="OBJECTIVE">We sought to test the content validity of a new training model for flexible ureteroscopy: the Key-Box.</AbstractText>
      <AbstractText Label="MATERIAL AND METHODS" NlmCategory="METHODS">Sixteen medical students were randomized to undergo a 10-day training consisting of performing 10 different exercises aimed at learning specific movements with the flexible ureteroscope, and how to catch and release stones with a nitinol basket using the Key-Box (n&#x2009;=&#x2009;8 students in the training group, n&#x2009;=&#x2009;8 students in the nontraining control group). Subsequently, an expert endourologist (O.T.) blindly assessed skills acquired by the whole cohort of students through two exercises on ureteroscope manipulation and one exercise on stone capture selected among those used for the training. A performance scale (1-5) assessing different steps of the procedure was used to evaluate each student. Time to complete the exercises was measured. Mann-Whitney Rank Sum test was used for comparisons between the two groups.</AbstractText>
      <AbstractText Label="RESULTS" NlmCategory="RESULTS">Mean scores obtained by trained students were significantly higher compared with those obtained by nontrained students (all p&#x2009;&lt;&#x2009;0.001). All trained students were able to complete the two exercises on ureteroscope manipulation within 3 minutes, whereas two students (25%) were not able to finish the exercise on stone capture. Conversely, four (50%) and six (75%) nontrained students were not able to finish one out of the two exercises on ureteroscope manipulation and the exercise on stone capture, respectively. The mean time to complete the three exercises was 76.3, 69.9, and 107 and 172.5, 137.9, and 168 seconds in the trained and nontrained groups, respectively (all p&#x2009;&lt;&#x2009;0.001).</AbstractText>
      <AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The K-Box(&#xAE;) seems to be a valid easy-to-use training model for initiating novel endoscopists to flexible ureteroscopy.</AbstractText>
    </Abstract>
    <AuthorList CompleteYN="Y">
      <Author ValidYN="Y">
        <LastName>Villa</LastName>
        <ForeName>Luca</ForeName>
        <Initials>L</Initials>
        <AffiliationInfo>
          <Affiliation>1 Division of Experimental Oncology/Unit of Urology, URI , IRCCS Ospedale San Raffaele, Milan, Italy .</Affiliation>
        </AffiliationInfo>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>&#x15E;ener</LastName>
        <ForeName>Tarik Emre</ForeName>
        <Initials>TE</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
        <AffiliationInfo>
          <Affiliation>3 Department of Urology, Marmara University School of Medicine , Istanbul, Turkey .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Somani</LastName>
        <ForeName>Bhaskar K</ForeName>
        <Initials>BK</Initials>
        <AffiliationInfo>
          <Affiliation>4 Department of Urology, University Hospital Southampton NHS Trust , Southampton, United Kingdom .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Cloutier</LastName>
        <ForeName>Jonathan</ForeName>
        <Initials>J</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
        <AffiliationInfo>
          <Affiliation>5 Department of Urology, University Hospital Centre of Quebec City , Quebec, Canada .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Buttic&#xE8;</LastName>
        <ForeName>Salvatore</ForeName>
        <Initials>S</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
        <AffiliationInfo>
          <Affiliation>6 Department of Urology, University of Messina , Messina, Italy .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Marson</LastName>
        <ForeName>Francesco</ForeName>
        <Initials>F</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
        <AffiliationInfo>
          <Affiliation>7 Department of Urology, Citt&#xE0; della Salute e della Scienza, Turin, Italy .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Doizi</LastName>
        <ForeName>Steeve</ForeName>
        <Initials>S</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Proietti</LastName>
        <ForeName>Silvia</ForeName>
        <Initials>S</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
        <AffiliationInfo>
          <Affiliation>8 Department of Urology, IRCCS San Raffaele Scientific Institute , Ville Turro Division, Milan, Italy .</Affiliation>
        </AffiliationInfo>
      </Author>
      <Author ValidYN="Y">
        <LastName>Traxer</LastName>
        <ForeName>Olivier</ForeName>
        <Initials>O</Initials>
        <AffiliationInfo>
          <Affiliation>2 Department of Urology, Tenon Hospital, Pierre and Marie Curie University , Paris, France .</Affiliation>
        </AffiliationInfo>
      </Author>
    </AuthorList>
    <Language>eng</Language>
    <PublicationTypeList>
      <PublicationType UI="D016428">Journal Article</PublicationType>
    </PublicationTypeList>
    <ArticleDate DateType="Electronic">
      <Year>2016</Year>
      <Month>12</Month>
      <Day>16</Day>
    </ArticleDate>
  </Article>
  <MedlineJournalInfo>
    <Country>United States</Country>
    <MedlineTA>J Endourol</MedlineTA>
    <NlmUniqueID>8807503</NlmUniqueID>
    <ISSNLinking>0892-7790</ISSNLinking>
  </MedlineJournalInfo>
  <KeywordList Owner="NOTNLM">
    <Keyword MajorTopicYN="N">flexible ureteroscopy</Keyword>
    <Keyword MajorTopicYN="N">learning curve</Keyword>
    <Keyword MajorTopicYN="N">training model</Keyword>
    <Keyword MajorTopicYN="N">ureteroscopy curriculum</Keyword>
  </KeywordList>
</MedlineCitation>
<PubmedData>
  <History>
    <PubMedPubDate PubStatus="pubmed">
      <Year>2016</Year>
      <Month>11</Month>
      <Day>22</Day>
      <Hour>6</Hour>
      <Minute>0</Minute>
    </PubMedPubDate>
    <PubMedPubDate PubStatus="medline">
      <Year>2016</Year>
      <Month>11</Month>
      <Day>22</Day>
      <Hour>6</Hour>
      <Minute>0</Minute>
    </PubMedPubDate>
    <PubMedPubDate PubStatus="entrez">
      <Year>2016</Year>
      <Month>11</Month>
      <Day>22</Day>
      <Hour>6</Hour>
      <Minute>0</Minute>
    </PubMedPubDate>
  </History>
  <PublicationStatus>ppublish</PublicationStatus>
  <ArticleIdList>
    <ArticleId IdType="pubmed">27869504</ArticleId>
    <ArticleId IdType="doi">10.1089/end.2016.0677</ArticleId>
  </ArticleIdList>
 </PubmedData>
</PubmedArticle>
</PubmedArticleSet>

Following is a code that I am using which works well except when there are multiple affiliations for authors of an article in PubMed database:

 library(rentrez)
 library(XML)

 pubmedSearch <- entrez_search("pubmed", term = "flexible ureteroscope Simulation Model", 
                          retmax = 10)
 SearchResults <- entrez_fetch(db="pubmed", pubmedSearch$ids, rettype="xml", 
                          parsed=TRUE)

 xmlGetValue <- function(x, node){
   a <- xpathSApply(x, node, xmlValue)
   if(length(a) == 0) {a <- NA} else {a}
 }

 parse_paper <- function(paper){
    pmid <- xmlGetValue(paper, ".//ArticleId[@IdType='pubmed']")
    first_names <- xmlGetValue(paper, ".//Author/ForeName")
    last_names <- xmlGetValue(paper, ".//Author/LastName")
    affiliation <- xmlGetValue(paper, ".//AffiliationInfo/Affiliation")
    data.frame(pmid=pmid, first_names=first_names, last_names=last_names,
         affiliation=affiliation)
 }  

parse_multiple_papers <- function(papers){
  res <- xpathApply(papers, "/PubmedArticleSet/*", parse_paper)
  do.call(rbind.data.frame, res)
}

test_df <- parse_multiple_papers(SearchResults)

Any help and support is really appreciated.

Solution

  • This question also came up as an issue @ rentrez's repository, details of one possible solution are given there. I'll include that code here too 

    parse_author <- function(author){
  fn  <- xmlValue(author[["ForeName"]])
  ln  <- xmlValue(author[["LastName"]])
  aff <-paste(xpathApply(author, "AffiliationInfo/Affiliation", xmlValue), collapse="; ")
  list(forname=fn, lastname=ln, affiliation=aff)
}

parse_paper <- function(paper){
  author_info <- xpathApply(paper, ".//AuthorList/Author", parse_author)
  res <- do.call(rbind.data.frame, author_info)
  res$pmid <-xpathSApply(paper, ".//ArticleId[@IdType='pubmed']", xmlValue)
  res
}

parse_multiple_papers <- function(papers){
 res <- xpathApply(papers, "/PubmedArticleSet/*", parse_paper)
 do.call(rbind.data.frame, res)
}

head(parse_multiple_papers(SearchResults))