Last updated: 2025-09-07
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Knit directory:
genomics_ancest_disease_dispar/
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knitr::opts_chunk$set(echo = TRUE,
message = FALSE,
warning = FALSE
)
library(data.table)
library(dplyr)
library(ggplot2)
library(stringr)library(httr)
library(jsonlite)url <-
"http://www.ebi.ac.uk/ols4/api/ontologies/mondo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0700096/descendants"
mondo_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
mondo_descendants <- c(mondo_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(mondo_descendants)
mondo_descendants[1:5]
writeLines(mondo_descendants, here::here("output/trait_ontology/mondo_0700096_descendants.txt"))url <-
"http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000408/descendants"
efo_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
efo_descendants <- c(efo_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(efo_descendants)
efo_descendants[1:5]
writeLines(efo_descendants, here::here("output/trait_ontology/efo_0000408_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/ncit/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCIT_C2991/descendants"
ncit_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
ncit_descendants <- c(ncit_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(ncit_descendants)
ncit_descendants[1:5]
writeLines(ncit_descendants, here::here("output/trait_ontology/ncit_C2991_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/ordo/terms/http%253A%252F%252Fwww.orpha.net%252FORDO%252FOrphanet_557493/descendants"
orphanet_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
orphanet_descendants <- c(orphanet_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(orphanet_descendants)
orphanet_descendants[1:5]
writeLines(orphanet_descendants, here::here("output/trait_ontology/orphanet_557493_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_1110122/descendants"
path_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
path_descendants <- c(path_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(path_descendants)
path_descendants[1:5]
writeLines(path_descendants, here::here("output/trait_ontology/obi_1110122_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOGMS_0000063/descendants"
disease_course_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
disease_course_descendants <- c(disease_course_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(disease_course_descendants)
disease_course_descendants[1:5]
writeLines(disease_course_descendants, here::here("output/trait_ontology/ogms_0000063_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/oba/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBA_2020000/descendants"
age_of_onset_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
age_of_onset_descendants <- c(age_of_onset_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(age_of_onset_descendants)
age_of_onset_descendants[1:5]
writeLines(age_of_onset_descendants, here::here("output/trait_ontology/oba_2020000_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHP_0000118/descendants"
hp_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
hp_descendants <- c(hp_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(hp_descendants)[1] 2625hp_descendants[1:5][1] "hypoxia"
[2] "necrosis"
[3] "Abnormality of limbs"
[4] "Abnormality of the musculoskeletal system"
[5] "Vocal cord dysfunction" hp_descendants = c(
"Abnormal aortic morphology",
"Abnormal chest sounds",
"Abnormality of the eye",
"Abnormal foot morphology",
"Abnormality of the gastrointestinal tract",
"Abnormality of the genital system",
"Abnormality of the liver",
"Abnormality of the nervous system",
"Abnormality of the skeletal system",
"Abnormality of the vasculature",
"Abnormal venous morphology",
hp_descendants)
hp_descendants = c("Phenotypic abnormality", hp_descendants)
writeLines(hp_descendants, here::here("output/trait_ontology/hp_0000118_descendants.txt"))# Define the API endpoint
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0001444/descendants"
measurement_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
measurement_descendants <- c(measurement_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(measurement_descendants)
measurement_descendants[1:5]
disease_measurement_grep_terms = c("age of onset",
"alcohol use",
"allergy",
"anemia (phenotype)",
"anxiety",
"cancer aggressiveness",
"coronary atherosclerosis",
"dependence",
"depressive",
"psoriasis 14,pustular",
"disease progression",
"disease severity",
"exacerbation",
"family history",
"food addiction",
"insomnia",
"lung disease",
"lewy body dementia",
"preeclampsia",
"rosacea",
"stroke outcome",
"sleep apnea",
"susceptibility to",
"symptom",
"oppositional defiant",
"withdrawal",
"psoriasis",
"psychosis"
)
disease_measurement_terms =
grep(pattern = paste0(disease_measurement_grep_terms, collapse = "|"),
measurement,
value = T
)
measurement_descendants = measurement_descendants[!measurement_descendants %in% disease_measurement_terms]
writeLines(measurement_descendants, here::here("output/trait_ontology/efo_0001444_descendants.txt"))
writeLines(disease_measurement_terms, here::here("output/trait_ontology/efo_0001444_disease_measurement_terms.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0004574/descendants"
total_choles_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
total_choles_descendants <- c(total_choles_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
writeLines(total_choles_descendants, here::here("output/trait_ontology/efo_0004574_descendants.txt"))
length(total_choles_descendants)
total_choles_descendants[1:5]Includes:
url <- "http://www.ebi.ac.uk/ols4/api/ontologies/go/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0050896/descendants"
go_response_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
go_response_descendants <- c(go_response_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(go_response_descendants)
go_response_descendants[1:5]
writeLines(go_response_descendants, here::here("output/trait_ontology/go_0050896_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0050896/descendants"
efo_response_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
efo_response_descendants <- c(efo_response_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(efo_response_descendants)
efo_response_descendants[1:5]
writeLines(efo_response_descendants, here::here("output/trait_ontology/efo_go_0050896_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000651/descendants"
phenotype_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
phenotype_descendants <- c(phenotype_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(phenotype_descendants)
phenotype_descendants[1:5]
writeLines(phenotype_descendants, here::here("output/trait_ontology/efo_0000651_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0004323/descendants"
mental_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
mental_descendants <- c(mental_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(mental_descendants)
mental_descendants[1:5]
mental_descendants = c("mental process",
"cognitive function measurement",
mental_descendants)
writeLines(mental_descendants, here::here("output/trait_ontology/efo_0004323_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FGO_0007610/descendants"
behavior_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
behavior_descendants <- c(behavior_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(behavior_descendants)
behavior_descendants[1:5]
behavior_descendants = c("behavior", behavior_descendants)
writeLines(behavior_descendants, here::here("output/trait_ontology/go_0007610_descendants.txt"))url <- "http://www.ebi.ac.uk/ols4/api/ontologies/efo/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000546/descendants"
injury_descendants <- c()
repeat {
res <- GET(url)
stop_for_status(res)
data <- fromJSON(content(res, as = "text", encoding = "UTF-8"))
injury_descendants <- c(injury_descendants, data$`_embedded`$terms$label)
# check if there is a next page
if (!is.null(data$`_links`$`next`$href)) {
url <- data$`_links`$`next`$href
} else {
break
}
}
length(injury_descendants)
injury_descendants[1:5]
injury_descendants = c("injury", injury_descendants)
writeLines(injury_descendants, here::here("output/trait_ontology/efo_0000546_descendants.txt"))enviro_factors <- c(
"income",
"socioeconomic status",
"encounter with health service related to socioeconomic and psychosocial circumstances" ,
"townsend deprivation index",
"household income",
"social deprivation",
"economic and social preference",
"social deprivation",
"physical activity",
"exercise",
"family relationship",
"cannabis use",
"alcohol drinking"
)
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] jsonlite_2.0.0 httr_1.4.7 stringr_1.5.1 ggplot2_3.5.2
[5] dplyr_1.1.4 data.table_1.17.8 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 compiler_4.3.1 renv_1.0.3 promises_1.3.3
[5] tidyselect_1.2.1 Rcpp_1.1.0 git2r_0.36.2 callr_3.7.6
[9] later_1.4.2 jquerylib_0.1.4 scales_1.4.0 yaml_2.3.10
[13] fastmap_1.2.0 here_1.0.1 R6_2.6.1 generics_0.1.4
[17] curl_6.4.0 knitr_1.50 tibble_3.3.0 rprojroot_2.1.0
[21] RColorBrewer_1.1-3 bslib_0.9.0 pillar_1.11.0 rlang_1.1.6
[25] cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16 xfun_0.52
[29] getPass_0.2-4 fs_1.6.6 sass_0.4.10 cli_3.6.5
[33] withr_3.0.2 magrittr_2.0.3 ps_1.9.1 grid_4.3.1
[37] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1 lifecycle_1.0.4
[41] vctrs_0.6.5 evaluate_1.0.4 glue_1.8.0 farver_2.1.2
[45] whisker_0.4.1 rmarkdown_2.29 tools_4.3.1 pkgconfig_2.0.3
[49] htmltools_0.5.8.1