In jaytimm/PubmedMTK: PubMed Mining Toolkit

A simple restructure of MeSH vocabulary

Intro

A clean & un-adulterated version of the MeSH hierarchical vocabulary & thesaurus as data frame. Included in the R package PumbedMTK. Based on two files: desc2021.xml & mtrees2021.bin; available via nlm.nih.gov.

git_dir <- '/home/jtimm/jt_work/GitHub/PubmedMTK/mesh/'

## Most recent data are available for downlaod below:
desc2020 <- 'ftp://nlmpubs.nlm.nih.gov/online/mesh/2020/xmlmesh/desc2021.xml'
trees2021 <- 'ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/meshtrees/mtrees2021.bin'

if (!require("pacman")) install.packages("pacman")
pacman::p_load(magrittr, dplyr, tidyr, xml2)

setwd(git_dir)
desc <- xml2::read_xml('desc2020.xml')
trees <- read.csv('mtrees2021.bin', header = FALSE, sep =';')

`desc` file

Extract descriptor details (& concepts & terms) from descriptor file.

## Descriptor
DescriptorUI <- desc %>% 
  xml2::xml_find_all('.//DescriptorUI') %>% 
  xml2::xml_text()

DescriptorName <- desc %>% 
  xml2::xml_find_all('.//DescriptorName') %>%  
  xml2::xml_text() 

descriptor <- data.frame(DescriptorUI, DescriptorName) %>%
  distinct() %>% 
  arrange(DescriptorUI)

## Concepts
ConceptName <- desc %>% 
  xml2::xml_find_all('.//ConceptName') %>%  
  xml2::xml_text()

ConceptUI <- desc %>% 
  xml2::xml_find_all('.//ConceptUI') %>%  
  xml2::xml_text()

concept <- data.frame(ConceptUI, ConceptName)

## Terms
TermUI <- desc %>% 
  xml2::xml_find_all('.//TermUI') %>%  
  xml2::xml_text() 

TermName <- desc %>% xml2::xml_find_all('.//Term') %>%  
  xml2::xml_find_all('String') %>%
  xml2::xml_text()

term <- data.frame(TermUI, TermName)

Note: Primary concept == primary term == descriptor name == mesh term.

concept_term <- term %>%

  left_join(concept, by = c('TermName' = 'ConceptName')) %>%
  fill(ConceptUI) %>%

  left_join(descriptor, by = c('TermName' = 'DescriptorName')) %>%

  mutate(DescriptorName = ifelse(is.na(DescriptorUI), NA, TermName)) %>%

  fill(DescriptorUI, DescriptorName) %>%
  select(DescriptorUI, DescriptorName, ConceptUI,
         TermUI, TermName)

`mtrees` file

tree <- trees %>%
  rename(mesh_heading = V1,
         tree_location = V2) %>%
  select(tree_location, mesh_heading)


# Extract the two highest parent nodes from tree location.  
## For general classification purposes.  

level1 <- tree[nchar(tree$tree_location) == 3, ]
level2 <- tree[nchar(tree$tree_location) == 7, ] %>%
  mutate(join = gsub('\\....', '', tree_location))

top_parents <- level2 %>%
  left_join(level1, by = c('join' = 'tree_location'))

colnames(top_parents) <- c('tree2', 'mesh2', 'tree1', 'mesh1')
top_parents <- top_parents[, c(3:4, 1:2)]

Manually add labels for highest-level node in hierarchy:

### 2-4 High-level categories
cats <- 
c('Anatomy', 'Organisms', 'Diseases', 'Chemicals and Drugs',
  'Analytical, Diagnostic and Therapeutic Techniques, and Equipment', 
  'Psychiatry and Psychology', 'Phenomena and Processes', 
  'Disciplines and Occupations', 
  'Anthropology, Education, Sociology, and Social Phenomena', 
  'Technology, Industry, and Agriculture', 'Humanities', 
  'Information Science', 'Named Groups', 'Health Care',
  'Publication Characteristics', 'Geographicals')

code <- c(LETTERS[1:14], 'V', 'Z')

high_tree <- data.frame(code, cats)

meta <- top_parents %>%
  mutate(code = gsub('..$', '', tree1)) %>%
  left_join(high_tree) %>%
  select(code:cats, tree1:mesh2)

Joining two data sets

Which adds the MeSH tree location to descriptor data via MeSH heading & DescriptorName variables. Note that a single DescriptorName may be classified (in tree structure) in multiple ways.

clean_col <- function(x) {
  x <- enc2utf8(x)
  x <- trimws(x)
  #x <- tolower(x)  
  }

### 2-5 Join metadata & descriptors/terms
pmtk_tbl_mesh <- concept_term %>%

  left_join(tree, by = c('DescriptorName' = 'mesh_heading')) %>%
  mutate (tree2 = substring(tree_location, 1, 7)) %>%

  left_join(meta) %>%

  # rename(descriptor_id = DescriptorUI,
  #        descriptor_name = DescriptorName,
  #        term_name = TermName) %>%

  select(DescriptorUI:DescriptorName, TermName, 
         code, cats,
         mesh1, mesh2,
         tree_location, tree1, tree2) %>%

  mutate_at(c('DescriptorName', 'TermName'), clean_col) %>%

  filter(complete.cases(.))

Sample records

knitr::kable(head(PubmedMTK::pmtk_tbl_mesh))

Output

pmtk_tbl_mesh <- data.table::data.table(pmtk_tbl_mesh)
setwd('/home/jtimm/jt_work/GitHub/PubmedMTK/data')
usethis::use_data(pmtk_tbl_mesh, overwrite=TRUE)

library(PubmedMTK)
data("pmtk_tbl_mesh")
data("pmtk_tbl_pmc_ref")
saveRDS(pmtk_tbl_mesh, '/home/jtimm/pCloudDrive/GitHub/packages/PubmedMTK/data-raw/pmtk_tbl_mesh.rds')
saveRDS(pmtk_tbl_pmc_ref, '/home/jtimm/pCloudDrive/GitHub/packages/PubmedMTK/data-raw/pmtk_tbl_pmc_ref.rds')