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Ignored files:
Ignored: .DS_Store
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Ignored: ancestry_dispar_env/
Ignored: author_manuscript.filelist.txt
Ignored: author_manuscript_files.txt
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Ignored: data/gbd/.DS_Store
Ignored: data/gbd/IHME-GBD_2021_DATA-d8cf695e-1.csv
Ignored: data/gbd/ihme_gbd_2019_global_disease_burden_rate_all_ages.csv
Ignored: data/gbd/ihme_gbd_2019_global_paf_rate_percent_all_ages.csv
Ignored: data/gbd/ihme_gbd_2021_global_disease_burden_rate_all_ages.csv
Ignored: data/gbd/ihme_gbd_2021_global_paf_rate_percent_all_ages.csv
Ignored: data/gwas_catalog/
Ignored: data/icd/.DS_Store
Ignored: data/icd/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX
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Ignored: data/icd/IHME_GBD_2021_COD_CAUSE_ICD_CODE_MAP_Y2024M05D16.XLSX
Ignored: data/icd/IHME_GBD_2021_NONFATAL_CAUSE_ICD_CODE_MAP_Y2024M05D16.XLSX
Ignored: data/icd/UK_Biobank_master_file.tsv
Ignored: data/icd/cdc_valid_icd10_Sep_23_2025.xlsx
Ignored: data/icd/cdc_valid_icd9_Sep_23_2025.xlsx
Ignored: data/icd/manual_disease_icd10_mappings.xlsx
Ignored: data/icd/phecode_international_version_unrolled.csv
Ignored: data/icd/semiautomatic_ICD-pheno.txt
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library(stringr)
library(readxl)
library(dplyr)
library(stringi)
library(rentrez)
library(xml2)
library(jsonlite)
# Improve sentence recognition
# library(reticulate)
# Path to the Python inside your venv
# python_path <- file.path(here::here(), "venv", "bin", "python") # Mac/Linux
# Sys.setenv(SPACY_PYTHON = python_path)
#
# use_python(Sys.getenv("SPACY_PYTHON",
# unset = "r-spacyr"), required = TRUE)
#
# # Check configuration
# py_config()
#
# py_module_available("spacy")
#
# library(spacyr)
# spacy_initialize(model = "en_core_web_sm")
# library(spacyr)
# reticulate::virtualenv_create("r-spacyr", python = python_exe)
# spacy_install(version = "apple")
# spacy_download_langmodel("en_core_web_sm")
library(tokenizers)## Step 1:
# get only disease studies
gwas_study_info <- data.table::fread(here::here("output/gwas_cat/gwas_study_info_trait_group_l2.csv"))
gwas_study_info = gwas_study_info |>
dplyr::rename_with(~ gsub(" ", "_", .x))
gwas_study_info =
gwas_study_info |>
dplyr::filter(DISEASE_STUDY == T) |>
dplyr::select(-COHORT)gwas_study_info_cohort =
data.table::fread(here::here("output/gwas_cohorts/gwas_cohort_name_corrected.csv"))
gwas_study_info_cohort =
gwas_study_info_cohort |>
dplyr::rename_with(~ gsub(" ", "_", .x))
gwas_study_info_cohort =
gwas_study_info_cohort |>
select(STUDY_ACCESSION,
COHORT) |>
distinct()
gwas_study_info =
left_join(gwas_study_info,
gwas_study_info_cohort,
by = "STUDY_ACCESSION"
)gwas_ancest_info <- data.table::fread(here::here("data/gwas_catalog/gwas-catalog-v1.0.3.1-ancestries-r2025-07-21.tsv"),
sep = "\t",
quote = "")
gwas_ancest_info = gwas_ancest_info |>
dplyr::rename_with(~ gsub(" ", "_", .x))
gwas_ancest_info =
gwas_ancest_info |>
select(STUDY_ACCESSION,
BROAD_ANCESTRAL_CATEGORY,
COUNTRY_OF_RECRUITMENT) |>
distinct() |>
group_by(STUDY_ACCESSION) |>
summarise(
BROAD_ANCESTRAL_CATEGORY = paste(
unique(
unlist(strsplit(BROAD_ANCESTRAL_CATEGORY, split = "\\|"))
),
collapse = "|"
),
COUNTRY_OF_RECRUITMENT = paste(
unique(
unlist(strsplit(COUNTRY_OF_RECRUITMENT, split = "\\|"))
),
collapse = "|"
)
)
gwas_study_info =
left_join(gwas_study_info,
gwas_ancest_info,
by = "STUDY_ACCESSION"
)gwas_study_info <-
gwas_study_info |>
#filter(COHORT != "") |>
select(PUBMED_ID,
COHORT,
DATE,
BROAD_ANCESTRAL_CATEGORY,
COUNTRY_OF_RECRUITMENT) |>
distinct() |>
group_by(PUBMED_ID,
DATE,
BROAD_ANCESTRAL_CATEGORY,
COUNTRY_OF_RECRUITMENT) |>
summarise(
COHORT = paste(
unique(
unlist(strsplit(COHORT, split = "\\|"))
),
collapse = "|"
)
)`summarise()` has grouped output by 'PUBMED_ID', 'DATE',
'BROAD_ANCESTRAL_CATEGORY'. You can override using the `.groups` argument.pmids = gwas_study_info$PUBMED_ID
cohort = gwas_study_info$COHORT
date = gwas_study_info$DATE
country = gwas_study_info$COUNTRY_OF_RECRUITMENT
ancestry = gwas_study_info$BROAD_ANCESTRAL_CATEGORY
# how many papers without cohort information
gwas_study_info |>
filter(COHORT == "") |>
nrow()[1] 4006# papers for which there is cohort information
gwas_study_info |>
filter(COHORT != "") |>
nrow()[1] 1626# Example PMIDs
rows_with_cohort = which(gwas_study_info$COHORT != "")
rows_without_cohort = which(gwas_study_info$COHORT == "")
rows =
c(rows_with_cohort,
sample(rows_without_cohort, length(rows_with_cohort))
)
pmids = pmids[rows]
cohort = cohort[rows]
names(cohort) = pmids
date = date[rows]
names(date) = pmids
country = country[rows]
names(country) = pmids
ancestry = ancestry[rows]
names(ancestry) = pmids# this xlsx was built from looking at acrynyms / cohort names in the gwas catalog
# and finding the corresponding full names / details of cohorts
cohort_names <- readxl::read_xlsx(here::here("data/cohort/cohort_desc.xlsx"),
sheet = 1)New names:
• `` -> `...13`cohort_full_names = cohort_names$full_name[!is.na(cohort_names$full_name)]
cohort_full_names <- str_trim(cohort_full_names)
cohort_full_names <- iconv(cohort_full_names, to = "UTF-8")
cohort_full_names <- gsub("[\u00A0\r\n]", " ", cohort_full_names) # replace non-breaking spaces, CR, LF with space
cohort_full_names <- str_squish(cohort_full_names) # trims and removes extra spaces
# sort by length of name (longest first) to match longest names first
cohort_full_names <- cohort_full_names[order(-nchar(cohort_full_names))]
cohort_full_names <- cohort_full_names[cohort_full_names != "Not Reported"]
cohort_abbr_names = cohort_names$cohort[!is.na(cohort_names$cohort)]
cohort_abbr_names <- str_trim(cohort_abbr_names)
cohort_abbr_names <- iconv(cohort_abbr_names, to = "UTF-8")
cohort_abbr_names <- gsub("[\u00A0\r\n]", " ", cohort_abbr_names) # replace non-breaking spaces, CR, LF with space
cohort_abbr_names <- str_squish(cohort_abbr_names) # trims and removes extra spaces
# remove abbreviations that are too short
cohort_abbr_names <- cohort_abbr_names[nchar(cohort_abbr_names) >= 4]
small_abbr_to_keep <- c("C4D",
"BBJ",
"UKB",
"MVP",
"TWB",
"QBB",
"MEC"
)
cohort_abbr_names <- unique(c(cohort_abbr_names,
small_abbr_to_keep
))
cohort_abbr_names <- cohort_abbr_names[!grepl("?", cohort_abbr_names)]
# sort by length of name (longest first) to match longest names first
cohort_abbr_names <- cohort_abbr_names[order(-nchar(cohort_abbr_names))]set_entrez_key(Sys.getenv('NCBI_API_KEY'))
get_pubmed_abstracts <- function(pmids,
batch_size = 200,
verbose = TRUE) {
n <- length(pmids)
abstracts <- setNames(rep("MISSING",
n),
pmids
) # initialize result
# Split PMIDs into batches
batches <- split(pmids,
ceiling(seq_along(pmids)/batch_size)
)
for(i in seq_along(batches)) {
batch_pmids <- batches[[i]]
if(verbose) message(sprintf("Fetching batch %d of %d (%d PMIDs)...",
i,
length(batches),
length(batch_pmids)
)
)
# Fetch XML
xml_data <- entrez_fetch(db = "pubmed",
id = paste(batch_pmids,
collapse = ","),
rettype = "xml",
parsed = FALSE
)
doc <- read_xml(xml_data)
articles <- xml_find_all(doc, ".//PubmedArticle")
for(article in articles) {
pmid_node <- xml_find_first(article,
".//PMID")
pmid <- xml_text(pmid_node)
abstract_nodes <- xml_find_all(article,
".//AbstractText")
if(length(abstract_nodes) > 0) {
abstracts[pmid] <- paste(xml_text(abstract_nodes),
collapse = " ")
}
}
}
return(abstracts)
}
pmids = unique(pmids)
abstracts <- get_pubmed_abstracts(pmids)
pmids <- pmids[abstracts != "MISSING"]
date <- date[abstracts != "MISSING"]
cohort <- cohort[abstracts != "MISSING"]
abstracts <- abstracts[abstracts != "MISSING"]
# Loop through abstracts and write each to a file
for (i in seq_along(abstracts)) {
file_name <- paste0(here::here("output/abstracts/"), pmids[i], ".txt")
writeLines(abstracts[i], file_name)
}abstract_files <- list.files(here::here("output/abstracts/"),
pattern = "*.txt",
full.names = FALSE
)
pmids_with_abstracts = gsub("\\.txt$", "", abstract_files)
all_pmids = gwas_study_info$PUBMED_ID |> unique()
missing_abstracts = setdiff(all_pmids,
pmids_with_abstracts)
print("Number of missing abstracts:")[1] "Number of missing abstracts:"length(missing_abstracts)[1] 42library(openalexR)
# get information on these papers from openAlex
oa_example <-
oa_fetch(entity = "works",
pmid = missing_abstracts,
abstract = TRUE)
oa_example |>
select(doi, abstract) |>
distinct()# A tibble: 41 × 2
doi abstract
<chr> <chr>
1 https://doi.org/10.1038/s41431-020-0636-6 <NA>
2 https://doi.org/10.1038/s41586-022-04826-7 <NA>
3 https://doi.org/10.1038/mp.2009.107 <NA>
4 https://doi.org/10.1016/j.jaci.2015.01.047 <NA>
5 https://doi.org/10.1002/art.23603 <NA>
6 https://doi.org/10.1016/j.jaci.2010.06.051 <NA>
7 https://doi.org/10.1176/appi.ajp.2013.12091228 <NA>
8 https://doi.org/10.1164/rccm.202206-1139le "\"Identification of a Genet…
9 https://doi.org/10.1161/circgenetics.111.960989 <NA>
10 https://doi.org/10.4088/jcp.15l10127 "Article Abstract Because th…
# ℹ 31 more rowsabstracts <- sapply(abstract_files,
function(file) {
readLines(here::here(paste0("output/abstracts/",file)),
warn = FALSE) |>
paste(collapse = " ")
}
)
pmids = pmids_with_abstracts
cohort = cohort[pmids]
date = date[pmids]
country = country[pmids]extract_cohort_sentences <- function(text_vector,
cohort_names,
ignore_case) {
results <- lapply(seq_along(text_vector), function(i) {
abstract <- text_vector[i]
# Split abstract into sentences
sentences <- unlist(tokenize_sentences(abstract))
# For each sentence, find all matching cohort names
lapply(seq_along(sentences), function(s) {
sentence <- sentences[s]
# Identify cohort names present in this sentence
matched_cohorts <- cohort_names[str_detect(sentence,
regex(cohort_names,
ignore_case = ignore_case))]
data.frame(
abstract_id = i,
sentence_id = s,
sentence = sentence,
has_cohort = length(matched_cohorts) > 0,
COHORT = if (length(matched_cohorts) > 0) str_flatten(unique(matched_cohorts), collapse = "|", na.rm = T) else "",
stringsAsFactors = FALSE
)
}) |> bind_rows()
})
bind_rows(results)
}
cohort_sentences_df <- extract_cohort_sentences(abstracts,
cohort_full_names,
ignore_case = TRUE
)
cohort_sentences_df_p2 = extract_cohort_sentences(abstracts,
cohort_abbr_names,
ignore_case = FALSE
)
cohort_sentences_df =
bind_rows(cohort_sentences_df,
cohort_sentences_df_p2
)
cohort_sentences_df =
cohort_sentences_df |>
distinct()# set the ratio of sentences with/without cohort names
# ratio = 1
#
# # number of sentences with cohort names
# n_tp_sentences = nrow(cohort_sentences_df |>
# filter(COHORT != "")
# )
# cohort_sentences_df =
# cohort_sentences_df |>
# mutate(has_cohort = ifelse(COHORT == "", FALSE, TRUE)) |>
# group_by(has_cohort) |>
# slice_sample(n = ratio*n_tp_sentences,
# replace = FALSE
# )
filtered_cohort_sentences_df =
cohort_sentences_df |>
filter(COHORT != "")
control_cohort_sentences_df <-
cohort_sentences_df |>
filter(grepl("cohort|consortium|study|population|registry|biobank|corsortia",
sentence,
ignore.case = TRUE)
) |>
slice_sample(n = 1000)
filtered_cohort_sentences_df =
bind_rows(filtered_cohort_sentences_df,
control_cohort_sentences_df
) |>
distinct()
filtered_cohort_sentences_df =
filtered_cohort_sentences_df |>
group_by(abstract_id, sentence_id, sentence) |>
summarise(
COHORT = str_flatten(unique(COHORT), collapse = "|", na.rm = T)
) |>
ungroup()`summarise()` has grouped output by 'abstract_id', 'sentence_id'. You can
override using the `.groups` argument.abstract_ids = filtered_cohort_sentences_df$abstract_id |> unique() |> sort()
pmids = pmids[abstract_ids]
abstracts = abstracts[abstract_ids]
date = date[abstract_ids]
cohort = cohort[abstract_ids]# file path for intermediate json file output
json_file = here::here("output/doccano/abstracts_with_cohort_info.json")
# file path for final jsonl file output
jsonl_file = here::here("output/doccano/abstracts_with_cohort_info.jsonl")
convert_to_doccano_json_sentence_level <- function(pmids,
date,
cohort,
country,
cohort_sentences_df) {
# set up json list
doccano_list <- list()
example_id <- 1
for(current_sentence in cohort_sentences_df$sentence) {
# Filter cohort sentences that match this sentence (safe matching)
df <- cohort_sentences_df |>
dplyr::filter(sentence == current_sentence)
# abstract_id <- df$abstract_id
# matched_cohort <- df$COHORT
for (i in seq_len(nrow(df))) {
matched_cohort <- df$COHORT[i]
abstract_id <- df$abstract_id[i]
#browser()
if(matched_cohort == ""){
doccano_list[[example_id]] <- list(
text = current_sentence,
pubmed_id = pmids[abstract_id],
date = date[abstract_id],
country = country[abstract_id],
gwas_cat_cohort_label = cohort[abstract_id],
label = list()
)
} else {
# Find the location of all matches of the cohort name in the sentence
if(grepl("\\|", matched_cohort)) {
# If multiple cohort names, separate
matched_cohort <- unlist(
strsplit(matched_cohort,
split = "\\|")
)
match_locations <- list()
for(current_matched_cohort in matched_cohort){
matches <- str_locate_all(current_sentence,
fixed(current_matched_cohort,
ignore_case = TRUE)
)[[1]]
match_locations <- append(match_locations,
list(matches)
)
}
# Combine all match locations into a single matrix
matches <- do.call(rbind, match_locations)
} else {
matches <- str_locate_all(current_sentence,
fixed(matched_cohort,
ignore_case = TRUE)
)[[1]]
}
# Convert matches to 0-based indexing (for doccano)
matches[, "start"] <- matches[, "start"] - 1
# Turn match locations into entity list
entities <- list()
for(k in seq_len(nrow(matches))) {
entities <- append(entities, list(list(
start_offset = matches[k, "start"],
end_offset = matches[k, "end"],
label = "COHORT"
)))
}
# Create Doccano JSON entry
doccano_list[[example_id]] <- list(
# id = example_id,
text = current_sentence,
pubmed_id = pmids[abstract_id],
date = date[abstract_id],
country = country[abstract_id],
gwas_cat_cohort_label = cohort[abstract_id],
label = entities
)
}
}
example_id <- example_id + 1
}
# Suppose each element of json_list has 'labels' as a list of named lists
doccano_list <- lapply(doccano_list, function(x) {
x$label <- lapply(x$label, function(l) {
# convert named list to vector/list format [start, end, label]
c(l$start_offset, l$end_offset, l$label)
})
x
})
return(doccano_list)
}
# Create JSON as a list
json_list <- convert_to_doccano_json_sentence_level(pmids = pmids,
date = date,
cohort = cohort,
country = country,
filtered_cohort_sentences_df)
# Write to JSON file
writeLines(toJSON(json_list,
auto_unbox = TRUE,
pretty = TRUE),
json_file)
json_data <- fromJSON(json_file,
simplifyVector = FALSE)
# Open connection to JSONL file
con <- file(jsonl_file, "w")
# Loop over each element (object) and write as one line
for (i in seq_along(json_data)) {
writeLines(toJSON(json_data[[i]], auto_unbox = TRUE), con)
}
# Close connection
close(con)
cat("JSONL saved to:", jsonl_file, "\n")JSONL saved to: /Users/ibeasley/code/genomics_ancest_disease_dispar/output/doccano/abstracts_with_cohort_info.jsonl
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] openalexR_2.0.1 tokenizers_0.3.0 jsonlite_2.0.0 xml2_1.4.0
[5] rentrez_1.2.4 stringi_1.8.7 dplyr_1.1.4 readxl_1.4.5
[9] stringr_1.5.2 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] compiler_4.3.1 renv_1.0.3 promises_1.3.3 tidyselect_1.2.1
[5] Rcpp_1.1.0 git2r_0.36.2 callr_3.7.6 later_1.4.4
[9] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0 here_1.0.1
[13] R6_2.6.1 SnowballC_0.7.1 generics_0.1.4 curl_7.0.0
[17] knitr_1.50 XML_3.99-0.19 tibble_3.3.0 rprojroot_2.1.0
[21] bslib_0.9.0 pillar_1.11.1 rlang_1.1.6 utf8_1.2.6
[25] cachem_1.1.0 httpuv_1.6.16 xfun_0.53 getPass_0.2-4
[29] fs_1.6.6 sass_0.4.10 cli_3.6.5 withr_3.0.2
[33] magrittr_2.0.4 ps_1.9.1 digest_0.6.37 processx_3.8.6
[37] rstudioapi_0.17.1 lifecycle_1.0.4 vctrs_0.6.5 data.table_1.17.8
[41] evaluate_1.0.5 glue_1.8.0 whisker_0.4.1 cellranger_1.1.0
[45] rmarkdown_2.30 httr_1.4.7 tools_4.3.1 pkgconfig_2.0.3
[49] htmltools_0.5.8.1