Parse multiple element XML values into a R dataframe

Question

I have an XML like:

    <Trait ID="4711" Type="Disease">
    <!--  each phenotype -->
    <Name>
    <ElementValue Type="Preferred">Breast-ovarian cancer, familial 1</ElementValue>
    <XRef ID="Breast-ovarian+cancer%2C+familial+1/7865" DB="Genetic Alliance"/>
    </Name>
    <Name>
    <ElementValue Type="Alternate">BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1</ElementValue>
    <XRef Type="MIM" ID="604370" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0001" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0002" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0003" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0004" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0005" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0006" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0007" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0008" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0009" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0010" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0011" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0012" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0013" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0014" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0015" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0016" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0017" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0018" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0019" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0020" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0021" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0022" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0023" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0024" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0025" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0026" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0027" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0028" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0029" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0030" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0031" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0032" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0033" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0034" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0035" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0036" DB="OMIM"/>
    <XRef Type="Allelic variant" ID="113705.0037" DB="OMIM"/>
    </Name>
    <Name>
    <ElementValue Type="Alternate">OVARIAN CANCER, SUSCEPTIBILITY TO</ElementValue>
    <XRef Type="Allelic variant" ID="602667.0001" DB="OMIM"/>
    </Name>
    <Name>
    <ElementValue Type="Alternate">BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1</ElementValue>
    <XRef ID="604370" DB="OMIM"/>
    </Name>
    <Name>
    <ElementValue Type="Alternate">Breast cancer, familial 1</ElementValue>
    </Name>
    <Name>
    <ElementValue Type="Alternate">Breast-ovarian cancer, familial 1 and 2</ElementValue>
    <XRef ID="GTR000310494" DB="Laboratory of Genetics,HUSLAB"/>
    </Name>
    <Name>
    <ElementValue Type="Alternate">BRCA1 Gene Mutation</ElementValue>
    <XRef ID="GTR000501743" DB="Myriad Genetic Laboratories,Myriad Genetic Laboratories, Inc."/>
    </Name>
</Trait>

And I want to parse the XML to a data frame like:

enter image description here

Im tring to use the r package XML, but the problem that i have more XREF attribute values than names of trait values. I can solve this with a for loop but that is often not the "R way". I was wondering if, there are is a simpler solution? (e.g. with xpath query).

I'm trying something like this:

x <- do.call(rbind, xpathApply(xml_1, "//TraitSet/Trait[@ID='4711']/Name", function(node) {
  
  trait <- xmlValue(node[["ElementValue"]])
  
  xp <- "//TraitSet/Trait[@ID='4711']/Name/XRef"
  DB <- sapply(c("ID","DB"), function(x) xpathSApply(xmltop, '//TraitSet/Trait/Name/XRef', xmlGetAttr, x))
  if (is.null(DB)) DB <- NA
  
  data.frame(trait, DB, stringsAsFactors = FALSE)
  
}))

but the records are incorrectly multiplied.

I will appreciate help! Thanks

Guillaume · Accepted Answer · 2022-01-23 23:09:00Z

This is a solution I think with xml2 and a quick and verbose tidy verse approach.

Not always easy to have a compact code when importing nested xml data.


library(xml2)
library(dplyr)
library(tidyr)
library(purrr)

# read the xml file
te <- xml2::read_xml("~/Desktop/test_so.xml")

# to move from node to node
cursor <- xml2::xml_find_all(te, ".//Name")

# i <- 1L
seq_along(cursor) %>% 
  # map to move along cursor
  purrr::map_df(function(i){
    print(i)
    x <- cursor[i]
    # first part is Name and Type (Alternate/Disease/Preferred)
    dplyr::tibble(Type = xml2::xml_attr(xml_find_all(x, './/ElementValue'), 'Type'),
         Trait = xml2::xml_text(x)) -> temp
    
    # second part is not always here so test if it exists before, then
    # if it exists, extract and compact it (nest)
    if (!is.na(xml2::xml_text(xml2::xml_find_first(x, './/XRef')))){
      Details <- dplyr::tibble(
         DB = xml2::xml_find_all(x, './/XRef') %>% 
           xml2::xml_attr('DB'),
         ID = xml2::xml_find_all(x, './/XRef') %>% 
           xml2::xml_attr('ID'),
         Type_ = xml2::xml_find_all(x, './/XRef') %>% 
           xml2::xml_attr('Type')) %>% tidyr::nest(data = c('DB', 'ID', 'Type_'))
      } else {
      # if it doesn't exist, fill with an empty df and compact it too (nest)
      Details <- dplyr::tibble(DB = NA, ID = NA, Type_ = NA) %>% 
        tidyr::nest(data = c('DB', 'ID', 'Type_'))
      }
    # add this new "df" column to temporary object
    temp <- temp %>% dplyr::mutate(Details = Details$data)
    # return
    temp
  }) -> te2

result <- te2 %>% 
  unnest(Details)

# A tibble: 44 × 5
   Type      Trait                                                 DB               ID                                       Type_          
   <chr>     <chr>                                                 <chr>            <chr>                                    <chr>          
 1 Preferred Breast-ovarian cancer, familial 1                     Genetic Alliance Breast-ovarian+cancer%2C+familial+1/7865 NA             
 2 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             604370                                   MIM            
 3 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0001                              Allelic variant
 4 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0002                              Allelic variant
 5 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0003                              Allelic variant
 6 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0004                              Allelic variant
 7 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0005                              Allelic variant
 8 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0006                              Allelic variant
 9 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0007                              Allelic variant
10 Alternate BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1 OMIM             113705.0008                              Allelic variant
# … with 34 more rows
>

Its an excelent resolution @Guillaume ! This is very readable. Thank you!
thanks for the feedback. This code and your case will helps me too when I have to do the same kind of things at work.

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