mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 04:46:11 +01:00
59 lines
2.0 KiB
R
59 lines
2.0 KiB
R
|
|
# WORK IN PROGRESS --------------------------------------------------------
|
|
|
|
# vector with official names, return vector with CIDs
|
|
get_CID <- function(ab) {
|
|
CID <- rep(NA_integer_, length(ab))
|
|
p <- progress_estimated(n = length(ab), min_time = 0)
|
|
for (i in 1:length(ab)) {
|
|
p$tick()$print()
|
|
|
|
CID[i] <- tryCatch(
|
|
data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
|
|
ab[i],
|
|
"/cids/TXT?name_type=complete"),
|
|
showProgress = FALSE)[[1]][1],
|
|
error = function(e) NA_integer_)
|
|
Sys.sleep(0.2)
|
|
}
|
|
CID
|
|
}
|
|
|
|
# returns vector with synonyms (brand names) for a single CID
|
|
get_synonyms <- function(CID, clean = TRUE) {
|
|
p <- progress_estimated(n = length(CID), min_time = 0)
|
|
p$tick()$print()
|
|
|
|
synonyms_txt <- tryCatch(
|
|
data.table::fread(paste0("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
|
|
CID,
|
|
"/synonyms/TXT"),
|
|
sep = "\n",
|
|
showProgress = FALSE)[[1]],
|
|
error = function(e) NA_character_)
|
|
|
|
if (clean == TRUE) {
|
|
# remove txt between brackets
|
|
synonyms_txt <- trimws(gsub("[(].*[)]", "", gsub("[[].*[]]", "", synonyms_txt)))
|
|
# only length 6 to 20 and no txt with reading marks or numbers
|
|
synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(6:20)
|
|
& !synonyms_txt %like% "[-&{},_0-9]"]
|
|
synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
|
|
}
|
|
synonyms_txt <- synonyms_txt[tolower(synonyms_txt) %in% unique(tolower(synonyms_txt))]
|
|
sort(synonyms_txt)
|
|
}
|
|
|
|
CIDs <- get_CID(antibiotics$official)
|
|
synonyms <- character(length(CIDs))
|
|
p <- progress_estimated(n = length(synonyms), min_time = 0)
|
|
for (i in 365:length(synonyms)) {
|
|
#p$tick()$print()
|
|
if (!is.na(CIDs[i])) {
|
|
synonyms[i] <- paste(get_synonyms(CIDs[i]), collapse = "|")
|
|
}
|
|
}
|
|
|
|
antibiotics$cid <- CIDs
|
|
antibiotics$trade_name <- synonyms
|