# ============================================================================== # Generate code lists for BMI # Authors: SM Wu & S Picton # Date Created: 2026/03/10 # Date Updated: 2026/04/14 # # Details: # 1) Set up and load data # 2) Search for new relevant med codes # 3) Create updated code lists # 4) Adjust formatting for extraction # # Inputs: # 1) Code_Lists/MASTER_Lists/CPRD_Aurum_Medical_14Oct2025.txt: Aurum medical master code list # 2) Code_Lists/MASTER_Lists/CPRD_GOLD_Medical_14Oct2025.txt: GOLD medical master code list # 3) Code_Lists/BMI/Old/Aurum_BMI_20230724_Alvin.txt : Old Aurum BMI code list # 4) Code_Lists/BMI/Old/Gold_BMI_20230724_Alvin.txt : Old Gold BMI code list # # Final Outputs: # 1) Code_Lists/BMI/Aurum_BMI_codelist_20260320.txt : Updated Aurum BMI code list # 2) Code_Lists/BMI/Gold_BMI_codelist_20260320.txt : Updated Gold BMI code list # 3) Code_Lists/BMI/Aurum_Gold_BMI_codelist_20260320.txt : Updated combined Aurum & Gold code list # ================= 1) Set up and load data ==================================== # Clear memory rm(list = ls()) # Packages library(readr) library(dplyr) library(stringr) library(tidyr) # If working in Data Safe Haven - manually install packages using Artifactory: # bit, bit64, cli, crayon, dplyr, generics, glue, hms, # lifecycle, magrittr, pillar, pkgconfig, purrr, R6, readr, rlang, stringi, # stringr, tibble, tidyr, tidyselect, tzdb, utf8, vctrs, vroom, withr, writexl # ### For running locally # # Set working directory # wd <- "/Volumes/ritd-ag-project-rd00qv-jfhay18/" # VPN connection # # wd <- "//live.rd.ucl.ac.uk/ritd-ag-project-rd00qv-jfhay18/" #Desktop@UCL # setwd(wd) # # # Set input and output paths # path_input <- "Code_Lists/" # path_output <- "Code_Lists/BMI/" ### For running in Data Safe Haven # Set working directory wd <- "S:/CDSTP_CPRD_25_005368/" setwd(wd) # Set input and output paths path_input <- "SMI_GLP/Code_Lists/" path_output <- "SMI_GLP/Code_Lists/BMI/" ## Load data # Read in Aurum medical dictionary cprd_aurum_medical_raw <- read_delim( paste0(wd, path_input, "MASTER_Lists/CPRD_Aurum_Medical_14Oct2025.txt"), delim = "\t", escape_double = FALSE, col_types = cols(MedCodeId = col_character(), OriginalReadCode = col_character(), CleansedReadCode = col_character(), SnomedCTConceptId = col_character(), SnomedCTDescriptionId = col_character()), trim_ws = TRUE) cprd_aurum_medical <- cprd_aurum_medical_raw %>% select(-Release) %>% rename(term = Term, medcodeid = MedCodeId) %>% mutate(term = str_to_lower(term)) # Read in Gold medical dictionary cprd_gold_medical_raw <- read_delim( paste0(wd, path_input, "MASTER_Lists/CPRD_GOLD_Medical_14Oct2025.txt"), delim = "\t", escape_double = FALSE, col_types = cols(medcode = col_character(), readcode = col_character()), trim_ws = TRUE) cprd_gold_medical <- cprd_gold_medical_raw %>% rename(term = readterm) %>% mutate(term = str_to_lower(term)) # Read in old BMI code list from 2023/07/24, setting all col types to character # Aurum aurum_BMI_old <- read_delim( paste0(wd, path_input, "BMI/Old/Aurum_BMI_20230724_Alvin.txt"), delim = "\t", escape_double = FALSE, col_types = cols(medcodeid = col_character()), trim_ws = TRUE) # Gold gold_BMI_old <- read_delim( paste0(wd, path_input, "BMI/Old/Gold_BMI_20230724_Alvin.txt"), delim = "\t", escape_double = FALSE, col_types = cols(medcode = col_character()), trim_ws = TRUE) # ================= 2) Search for new relevant med codes ======================= # Aurum aurum_BMI <- cprd_aurum_medical %>% # Inclusion - BMI related terms, filter(grepl(paste0("(?i)BMI|weight|obesity|underweight|overweight|obese|height|body mass index"), term)) %>% # Exclusion - Unrelated terms filter(!grepl(paste0("(?i)below knee|weightless environment|weightlessness| weight-bearing|non-weight-bearing|sample|weight-bearing|weight-bear| post-dialysis|fpc|molecular|gold|heparin|hb|lift weights| lesions|7pcl|eyelid|7-point|skin lesion|ede-q|skeletal dysplasia| down's|mri|magnetic", # Unrelated height codes "uterine fundus|fundal|unfit|gravid|fall|jumping|tinetti| mid-parental|predicted|down's|footwear|measurement declined|furniture| heightened|falling|pubis|demispan|sitting|wave|fear|knee|neurodynamic| mother|perception|uterine|fundus|fundal|qrs|step", # Relating to family history "fh:obesity|family history:|fh:", # Relating to children "baby birth|child|infant|premature|baby|childhood|birthweight|birth| fetal|circum.|foetal|child protection conference|child weight=|27-30 mth exam.| national child measurement programme|child overweight|overweight child", # Negations "not done|unsuitable for", # Relating to pregnancy "pregnancy|gestation|placental|placenta|preg|postnatal|preg+postnatal| maternal", # Process of care "framingham", # Relating to eating disorder "purging|excessive exercise| self-induced purging", # Administrative "ede-q|compensation|ac563|see report|sentinel"), term, perl = TRUE)) %>% # Filter out fh code filter(!grepl("fh:[-_ ]*obesity", term, ignore.case = TRUE, perl = TRUE)) # Gold gold_BMI <- cprd_gold_medical %>% # Inclusion - BMI related terms, filter(grepl(paste0("(?i)BMI|weight|obesity|underweight|overweight|obese|height|body mass index"), term)) %>% # Exclusion - Unrelated terms filter(!grepl(paste0("(?i)below knee|weightless environment|weightlessness| weight-bearing|non-weight-bearing|sample|weight-bearing|weight-bear| post-dialysis|fpc|molecular|gold|heparin|hb|lift weights| lesions|7pcl|eyelid|7-point|skin lesion|ede-q|skeletal dysplasia| down's|mri|magenetic", # Unrelated height codes "uterine fundus|fundal|unfit|gravid|fall|jumping|tinetti| mid-parental|predicted|down's|footwear|measurement declined|furniture| heightened|falling|pubis|demispan|sitting|wave|fear|knee|neurodynamic| mother|perception|uterine|fundus|fundal|qrs|step|mid-parental", # Relating to family history "fh:obesity|family history:|fh:", # Relating to children "baby birth|child|infant|premature|baby|childhood|birthweight|birth| fetal|circum.|foetal|child protection conference|child weight=|27-30 mth exam.| national child measurement programme|child overweight|overweight child", # Negations "not done|unsuitable for", # Relating to pregnancy "pregnancy|gestation|placental|placenta|preg|postnatal|preg+postnatal| maternal", # Process of care "framingham", # Relating to eating disorder "purging|excessive exercise| self-induced purging", # Administrative "ede-q|compensation|ac563|see report|sentinel"), term, perl = TRUE)) %>% # Filter out fh code filter(!grepl("fh:[-_ ]*obesity", term, ignore.case = TRUE, perl = TRUE)) ## Comparing with older codelists # New codes not in old list new_aurum <- aurum_BMI %>% filter(!medcodeid %in% aurum_BMI_old$medcodeid) new_gold <- gold_BMI %>% filter(!medcode %in% gold_BMI_old$medcode) # Old codes not in new old list miss_new_aurum <- aurum_BMI_old %>% filter(!medcodeid %in% aurum_BMI$medcodeid) miss_new_gold <- gold_BMI_old %>% filter(!medcode %in% gold_BMI$medcode) # ================= 3) Create updated code lists =============================== # Create updated code lists # Aurum BMI_codelist_aurum_new <- aurum_BMI # Gold BMI_codelist_gold_new <- gold_BMI # Save updated code lists write.table(BMI_codelist_aurum_new, file = paste0(wd, path_output, "Aurum_BMI_codelist_20260320.txt"), sep = "\t", row.names = FALSE) write.table(BMI_codelist_gold_new, file = paste0(wd, path_output, "Gold_BMI_codelist_20260320.txt"), sep = "\t", row.names = FALSE) # Combine Aurum and GOLD updated code lists temp_aurum <- BMI_codelist_aurum_new %>% rename(medcode = medcodeid, readcode = CleansedReadCode) %>% select(medcode, term) temp_gold <- BMI_codelist_gold_new %>% select(medcode, term) temp_both <- rbind(temp_aurum, temp_gold) aurum_gold_BMI_new <- temp_both %>% distinct() # # Combine Aurum and GOLD into one file with a column specifying database BMI_codelist_aurum_new$database <- "Aurum" BMI_codelist_gold_new$database <- "Gold" BMI_codelist_aurum_gold_new <- rbind( BMI_codelist_aurum_new %>% rename(medcode = medcodeid) %>% select(medcode, term, database), BMI_codelist_gold_new %>% select(medcode, term, database)) # # Save combined code list write.table(BMI_codelist_aurum_gold_new, file = paste0(wd, path_output, "Aurum_Gold_BMI_codelist_20260320.txt"), sep = "\t", row.names = FALSE)