# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:
library(plyr)
library(dplyr)
library(stringr)
library(readr)
library(purrr)
library(xml2)
library(BioChemPantry)
#####################################
# Analysis parameters
schema <- "hmdb_180122"
staging_directory <- BioChemPantry::get_staging_directory(schema)
dir.create(paste0(staging_directory, "/data"))
z_data <- readr::read_tsv(paste0(staging_directory, "/data/hmdbendo_substances.tsv"))
# input paths
hmdb_metabolites_xml <- paste0(staging_directory, "/dump/hmdb_metabolites.xml") %>%
xml2::read_xml()
xml_child_by_name <- function(xml, name){
child_index <- xml %>%
xml2::xml_children() %>%
xml2::xml_name() %>%
magrittr::equals(name) %>%
which
if(length(child_index) == 0) return(NA)
xml %>%
xml2::xml_children() %>%
magrittr::extract2(child_index)
}
# this takes several hours to run
m_data <- hmdb_metabolites_xml %>%
xml2::xml_children() %>%
plyr::ldply(function(metabolite){
get_value <- function(name){
node <- metabolite %>% xml_child_by_name(name)
if(is.na(node)) return(NA)
contents <- node %>% xml2::xml_contents()
if(length(contents) == 0) return(NA)
contents %>% as.character
}
get_taxon <- function(level){
taxonomy <- metabolite %>% xml_child_by_name("taxonomy")
if(is.na(taxonomy)) return(NA)
node <- taxonomy %>% xml_child_by_name(level)
if(is.na(node)) return(NA)
contents <- node %>% xml2::xml_contents()
if(length(contents) == 0) return(NA)
contents %>% as.character
}
ontology_status <- function(){
ontology_node <- metabolite %>% xml_child_by_name("ontology")
if(is.na(ontology_node)) return(NA)
status <- ontology_node %>% xml_child_by_name("status")
if(is.na(status)) return(NA)
contents <- status %>% xml2::xml_contents()
if(length(contents) == 0) return(NA)
contents %>% as.character
}
from_origin <- function(source){
ontology_node <- metabolite %>% xml_child_by_name("ontology")
if(is.na(ontology_node)) return(NA)
origins_nodeset <- ontology_node %>% xml_child_by_name("origins")
if(is.na(origins_nodeset) || length(origins_nodeset) == 0) return(NA)
origins <- origins_nodeset %>% xml2::as_list() %>% purrr::flatten
source %in% origins
}
tibble::data_frame(
accession = get_value("accession"),
name = get_value("name"),
smiles = get_value("smiles"),
description = get_value("description"),
taxonomy_description = get_taxon("description"),
taxonomy_kingdom = get_taxon("kingdom"),
taxonomy_super_class = get_taxon("super_class"),
taxonomy_class = get_taxon("class"),
taxonomy_sub_class = get_taxon("sub_class"),
taxonomy_molecular_framework = get_taxon("molecular_framework"),
ontology_status = ontology_status(),
origin_food = from_origin("Food"),
origin_endogenous = from_origin("Endogenous"),
origin_microbial = from_origin("Microbial"),
origin_drug = from_origin("Drug"),
origin_drug_or_steroid_metabolite = from_origin("Drug or Steroid Metabolite"),
origin_drug_metabolite = from_origin("Drug Metabolite"),
origin_plant = from_origin("Plant"),
origin_toxin_pollutant = from_origin("Toxin/Pollutant"),
origin_cosmetic = from_origin("Cosmetic"))
})
# HMDB classification, some compounds have an extra chemical entities layer at the top that provides no information
kingdom_is_chemical_entities <- m_data$taxonomy_kingdom == "Chemical entities"
m_data <- m_data %>%
dplyr::mutate(
taxonomy_kingdom = ifelse(kingdom_is_chemical_entities, taxonomy_super_class, taxonomy_kingdom),
taxonomy_super_class = ifelse(kingdom_is_chemical_entities, taxonomy_class, taxonomy_super_class),
taxonomy_class = ifelse(kingdom_is_chemical_entities, taxonomy_sub_class, taxonomy_class),
taxonomy_sub_class = ifelse(kingdom_is_chemical_entities, NA, taxonomy_sub_class))
m_data <- m_data %>%
dplyr::left_join(
z_data,
by=c("accession"))
m_data %>% readr::write_tsv(paste0(staging_directory, "/data/metabolites.tsv"))
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