mirror of
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110 lines
4.1 KiB
R
110 lines
4.1 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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library(AMR)
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library(tidyverse)
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# go to https://www.nictiz.nl/standaardisatie/terminologiecentrum/referentielijsten/micro-organismen/
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# read the table from clipboard
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snomed <- clipr::read_clip_tbl()
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# snomed <- snomed %>%
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# transmute(fullname = trimws(gsub("^genus", "", Omschrijving, ignore.case = TRUE)),
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# snomed = as.integer(Id))
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snomed <- snomed %>%
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transmute(fullname = mo_name(Omschrijving),
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snomed = as.integer(Id)) %>%
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filter(!fullname %like% "unknown")
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snomed_trans <- snomed %>%
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group_by(fullname) %>%
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mutate(snomed_list = list(snomed)) %>%
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ungroup() %>%
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select(fullname, snomed = snomed_list) %>%
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distinct(fullname, .keep_all = TRUE)
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microorganisms <- AMR::microorganisms %>%
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left_join(snomed_trans)
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# remove the NULLs, set to NA
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microorganisms$snomed <- lapply(microorganisms$snomed, function(x) if (length(x) == 0) NA else x)
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microorganisms <- dataset_UTF8_to_ASCII(microorganisms)
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usethis::use_data(microorganisms, overwrite = TRUE)
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rm(microorganisms)
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# OLD ---------------------------------------------------------------------
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baseUrl <- 'https://browser.ihtsdotools.org/snowstorm/snomed-ct'
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edition <- 'MAIN'
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version <- '2019-07-31'
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microorganisms.snomed <- data.frame(conceptid = character(0),
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mo = character(0),
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stringsAsFactors = FALSE)
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microorganisms$snomed <- ""
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# for (i in 1:50) {
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for (i in 1:1000) {
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if (i %% 10 == 0) {
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cat(paste0(i, " - ", cleaner::percentage(i / nrow(microorganisms)), "\n"))
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}
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mo_data <- microorganisms %>%
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filter(mo == microorganisms$mo[i]) %>%
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as.list()
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if (!mo_data$rank %in% c("genus", "species")) {
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next
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}
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searchTerm <- paste0(
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ifelse(mo_data$rank == "genus", "Genus ", ""),
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mo_data$fullname,
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" (organism)")
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url <- paste0(baseUrl, '/browser/',
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edition, '/',
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version,
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'/descriptions?term=', curl::curl_escape(searchTerm),
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'&mode=fullText&activeFilter=true&limit=', 250)
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results <- url %>%
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httr::GET() %>%
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httr::content(type = "text", encoding = "UTF-8") %>%
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jsonlite::fromJSON(flatten = TRUE) %>%
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.$items
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if (NROW(results) == 0) {
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next
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} else {
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message("Adding ", crayon::italic(mo_data$fullname))
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}
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tryCatch(
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microorganisms$snomed[i] <- results %>% filter(term == searchTerm) %>% pull(concept.conceptId),
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error = function(e) invisible()
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)
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if (nrow(results) > 1) {
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microorganisms.snomed <- microorganisms.snomed %>%
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bind_rows(tibble(conceptid = results %>% filter(term != searchTerm) %>% pull(concept.conceptId) %>% unique(),
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mo = as.character(mo_data$mo)))
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}
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}
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