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