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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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71
data-raw/reproduction_of_antibiotics.R
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@ -142,14 +142,15 @@ abx2 <- bind_rows(abx_atc1, abx_atc2)
rm(abx_atc1)
rm(abx_atc2)
abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(gsub(
"[/0-9-]",
" ",
abx2$name[is.na(abx2$ab)]
),
minlength = 3,
method = "left.kept",
strict = TRUE
abx2$ab[is.na(abx2$ab)] <- toupper(abbreviate(
gsub(
"[/0-9-]",
" ",
abx2$name[is.na(abx2$ab)]
),
minlength = 3,
method = "left.kept",
strict = TRUE
))
n_distinct(abx2$ab)
@ -197,24 +198,26 @@ get_CID <- function(ab) {
p$tick()
CID[i] <- tryCatch(
data.table::fread(paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
URLencode(ab[i], reserved = TRUE),
"/cids/TXT?name_type=complete"
),
showProgress = FALSE
data.table::fread(
paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
URLencode(ab[i], reserved = TRUE),
"/cids/TXT?name_type=complete"
),
showProgress = FALSE
)[[1]][1],
error = function(e) NA_integer_
)
if (is.na(CID[i])) {
# try with removing the text in brackets
CID[i] <- tryCatch(
data.table::fread(paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
"/cids/TXT?name_type=complete"
),
showProgress = FALSE
data.table::fread(
paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
URLencode(trimws(gsub("[(].*[)]", "", ab[i])), reserved = TRUE),
"/cids/TXT?name_type=complete"
),
showProgress = FALSE
)[[1]][1],
error = function(e) NA_integer_
)
@ -223,12 +226,13 @@ get_CID <- function(ab) {
# try match on word and take the lowest CID value (sorted)
ab[i] <- gsub("[^a-z0-9]+", " ", ab[i], ignore.case = TRUE)
CID[i] <- tryCatch(
data.table::fread(paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
URLencode(ab[i], reserved = TRUE),
"/cids/TXT?name_type=word"
),
showProgress = FALSE
data.table::fread(
paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/",
URLencode(ab[i], reserved = TRUE),
"/cids/TXT?name_type=word"
),
showProgress = FALSE
)[[1]][1],
error = function(e) NA_integer_
)
@ -260,13 +264,14 @@ get_synonyms <- function(CID, clean = TRUE) {
}
synonyms_txt <- tryCatch(
data.table::fread(paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
CID[i],
"/synonyms/TXT"
),
sep = "\n",
showProgress = FALSE
data.table::fread(
paste0(
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/cid/",
CID[i],
"/synonyms/TXT"
),
sep = "\n",
showProgress = FALSE
)[[1]],
error = function(e) NA_character_
)