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hpo_to_txt.R
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# script description ------------------------------------------------------
## Project: Ontologies
## Script: HPO_obo_to_txt.R
## Purpose: import Human Phenotype Ontology in obo format and convert it to
## to plain text files
# install / load libraries ------------------------------------------------
if (!require("ontologyIndex")) install.packages("ontologyIndex")
library("ontologyIndex")
if (!require("dplyr")) install.packages("dplyr")
library("dplyr")
if (!require("tidyr")) install.packages("tidyr")
library("tidyr")
if (!require("Hmisc")) install.packages("Hmisc")
library("Hmisc")
# get ontology ------------------------------------------------------------
hpo <- get_ontology("https://github.com/obophenotype/human-phenotype-ontology/releases/download/2025-01-16/hp-base.obo")
## hpo ids and descriptions
hpo_description <- data.frame(
hpo_term = as.character(row.names(as.data.frame(hpo[[2]]))),
hpo_description = as.character(as.data.frame(hpo[[2]])[, 1]),
stringsAsFactors = F)
## parents, children and all the ancetors for a given hpo term as a list
parents <- hpo[[3]]
children <- hpo[[4]]
ancestors <- hpo[[5]]
# set of functions to convert these lists to data frames ------------------
## get parental nodes
get_parent_nodes <- function(parents) {
hpo_term <- list()
hpo_parents <-list()
for(i in 1:length(names(parents))){
hpo_term [[i]] <- names(parents)[i]
hpo_parents[[i]] <- paste(parents[[i]], collapse=",")
}
hpo_parents <- data.frame(
hpo_term = do.call(rbind,hpo_term),
hpo_parents = do.call(rbind, hpo_parents), stringsAsFactors = F) %>%
mutate(hpo_parents = strsplit(as.character(hpo_parents), ",")) %>%
unnest(hpo_parents) %>%
filter(hpo_term != hpo_parents)
return(hpo_parents)
}
## get children nodes
get_children_nodes <- function(children) {
hpo_term <- list()
hpo_children <- list()
for(i in 1:length(names(children))){
hpo_term [[i]] <- names(children)[i]
hpo_children[[i]] <- paste(children[[i]], collapse=",")
}
hpo_children <- data.frame(
hpo_term = do.call(rbind, hpo_term),
hpo_children = do.call(rbind, hpo_children), stringsAsFactors = F) %>%
mutate(hpo_children = strsplit(as.character(hpo_children), ",")) %>%
unnest(hpo_children) %>%
filter(hpo_term != hpo_children)
return(hpo_children)
}
## get all the ancestors/ top levels
get_ancestor_nodes <- function(ancestors) {
hpo_term <- list()
hpo_ancestors <- list()
for(i in 1:length(names(ancestors))) {
hpo_term [[i]] <- names(ancestors)[i]
hpo_ancestors[[i]] <- paste(ancestors[[i]], collapse=",")
}
hpo_ancestors <- data.frame(
hpo_term = do.call(rbind, hpo_term),
hpo_ancestors = do.call(rbind, hpo_ancestors),stringsAsFactors = F) %>%
mutate(hpo_ancestors = strsplit(as.character(hpo_ancestors), ",")) %>%
unnest(hpo_ancestors) %>%
filter(hpo_term != hpo_ancestors )
return(hpo_ancestors)
}
## get top levels of the ontology (physiological systems)
hpo_toplevels <- get_parent_nodes(parents) %>%
filter(hpo_parents == "HP:0000001") %>%
left_join(hpo_description,by = "hpo_term") %>%
select(hpo_term, hpo_description)
hpo_toplevels_phenotypic_abnormalities_only <- get_parent_nodes(parents) %>%
filter(hpo_parents == "HP:0000118") %>%
left_join(hpo_description,by = "hpo_term") %>%
select(hpo_term,hpo_description)
# apply functions ---------------------------------------------------------
hpo_parental_nodes <- get_parent_nodes(parents)
hpo_children_nodes <- get_children_nodes(children)
hpo_ancestor_nodes <- get_ancestor_nodes(ancestors)
# export files ------------------------------------------------------------
hpo_dir <- "./data/"
files_to_export <- list(hpo_description,
hpo_parental_nodes,
hpo_children_nodes,
hpo_ancestor_nodes,
hpo_toplevels,
hpo_toplevels_phenotypic_abnormalities_only)
names(files_to_export) <- Cs(hpo_description,
hpo_parental_nodes,
hpo_children_nodes,
hpo_ancestor_nodes,
hpo_toplevels,
hpo_toplevels_phenotypic_abnormalities_only)
for (i in 1:length(files_to_export)){
write.table(files_to_export[[i]],
paste0(hpo_dir, names(files_to_export)[i], ".txt"),
quote = F, sep = "\t", row.names = FALSE)
}