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genomics_ancest_disease_dispar/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | b43e9a9 | IJbeasley | 2026-01-12 | Update getting full text |
| html | ac0d1a7 | IJbeasley | 2025-10-27 | Build site. |
| html | 8642872 | IJbeasley | 2025-10-27 | Build site. |
| Rmd | da4d730 | IJbeasley | 2025-10-27 | Now run on all texts |
| html | fb5cfd9 | IJbeasley | 2025-10-27 | Build site. |
| Rmd | 8ed4c37 | IJbeasley | 2025-10-27 | Now run on all texts |
| html | 8610283 | IJbeasley | 2025-10-27 | Build site. |
| Rmd | 7d504e3 | IJbeasley | 2025-10-27 | More fixing of download full text |
| html | 16f4c19 | IJbeasley | 2025-10-27 | Build site. |
| Rmd | 3df4096 | IJbeasley | 2025-10-27 | Update + improve full text downloading - test run |
| html | 1439951 | IJbeasley | 2025-10-24 | Build site. |
| Rmd | 481aebe | IJbeasley | 2025-10-24 | Update code for getting full texts |
library(httr)
library(xml2)
library(stringr)
library(here)
library(dplyr)
library(data.table)# gwas_study_info <- data.table::fread(here::here("output/gwas_cat/gwas_study_info_trait_group_l2.csv"))
## Step 1:
# get only relevant disease studies
# gwas_study_info <- data.table::fread(here::here("output/gwas_cat/gwas_study_info_trait_group_l2.csv"))
gwas_study_info <- data.table::fread(here::here("output/icd_map/gwas_study_gbd_causes.csv"))
gwas_study_info = gwas_study_info |>
dplyr::rename_with(~ gsub(" ", "_", .x))
# gwas_study_info <- gwas_study_info |>
# dplyr::filter(DISEASE_STUDY == TRUE)
pmids <- unique(gwas_study_info$PUBMED_ID)
#pmids <- sample(pmids, size = 500)
length(pmids)[1] 993# get PMID to PMCID mapping using Europe PMC file:
convert_pmid_df <- fread(here::here("data/europe_pmc/PMID_PMCID_DOI.csv"))Warning in fread(here::here("data/europe_pmc/PMID_PMCID_DOI.csv")): Found and
resolved improper quoting out-of-sample. First healed line 8637909:
<<17234576,PMC2742408,"https://doi.org/10.1102/1470-7330.2007.0001>>. If the
fields are not quoted (e.g. field separator does not appear within any field),
try quote="" to avoid this warning.convert_pmid_df <- convert_pmid_df |>
dplyr::rename(pmcids = PMCID
) |>
dplyr::mutate(pmcids = ifelse(is.na(pmcids),
"",
pmcids
)
)
convert_pmid_df =
convert_pmid_df |>
select(-DOI)
convert_pmid_df <-
convert_pmid_df |>
dplyr::filter(!is.na(PMID))
converted_ids =
convert_pmid_df |>
filter(PMID %in% pmids)
dim(converted_ids)[1] 993 2length(pmids)[1] 993converted_ids |>
filter(pmcids == "") |>
dim()[1] 202 2# convert PMID to PMCID
# convert_pmid_to_pmcid <- function(pmid_vec,
# tool = "myTool",
# email = "you@example.com",
# format = "json",
# batch_size = 50,
# sleep_time = 1) {
#
# base_url <- "https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/"
#
# batches <- split(pmid_vec,
# ceiling(seq_along(pmid_vec) / batch_size))
# #browser()
#
# pmcid_list = purrr::map(batches,
# function(pmid_vec) {
#
#
# ids_param <- paste(pmid_vec,
# collapse = ",")
#
# query <- list(ids = ids_param,
# idtype = "pmid",
# tool = tool,
# email = email,
# format = format
# )
#
# resp <- httr::GET(base_url,
# query = query)
#
# httr::stop_for_status(resp)
#
# content_text <- httr::content(resp,
# as = "text",
# encoding = "UTF-8")
#
# # Handle cases where records might be empty or missing pmcid
# parsed <- jsonlite::fromJSON(content_text,
# flatten = TRUE)
#
# parsed$records[is.na(parsed$records)] = ""
#
# pmcid <- parsed$records |>
# pull(pmcid)
#
# Sys.sleep(sleep_time)
#
# return(pmcid)
# }
# )
#
# pmcid_list = unlist(pmcid_list)
# names(pmcid_list) <- pmid_vec
# return(pmcid_list)
# }
#
# pmcids <- convert_pmid_to_pmcid(pmids)
#
# get_pmcid_europepmc <- function(pmid_vec) {
# base_url <- "https://www.ebi.ac.uk/europepmc/webservices/rest/search"
#
# purrr::map_dfr(pmid_vec, function(pmid) {
# query <- list(
# query = paste0("ext_id:", pmid),
# format = "json"
# )
# resp <- httr::GET(base_url, query = query)
# if (httr::status_code(resp) != 200) {
# return(tibble(pmid = pmid,
# pmcid = NA_character_))
# }
#
# dat <- jsonlite::fromJSON(httr::content(resp,
# as = "text",
# encoding = "UTF-8"))
#
# if (length(dat$resultList$result) == 0) {
# return(tibble(pmid = pmid, pmcid = NA_character_))
# }
#
# pmcid <- dat$resultList$result$pmcid
# tibble(pmid = pmid, pmcid = pmcid)
# })
# }
#
# pmids_missing = names(pmcids[pmcids == ""])
#
# get_pmcid_europepmc(pmids_missing) -> pmcid_europepmc_df
#
# converted_ids <-
# data.frame(pmids = names(pmcids),
# pmcids = pmcids
# )
#
# # checked using pmids to pmcs conversion from europe pmc webservice
# # can map 38367033 -> PMC12560237
# converted_ids <- converted_ids |>
# mutate(pmcids = ifelse(pmids == "38367033",
# "PMC12560237",
# pmcids
# )
# )
#
# data.table::fwrite(converted_ids,
# here::here("output/gwas_cat/gwas_pubmed_to_pmcid_mapping.csv")
# )
#
# # How many missing?
# sum(pmcids == "")
#
# pmcids <- pmcids[pmcids != ""]pmcids <-
converted_ids$pmcids |>
unique()
pmcids <- pmcids[pmcids != ""]
length(pmcids)[1] 791print("Percentage of pmids with pmcid:")[1] "Percentage of pmids with pmcid:"round(100 * length(pmcids) / length(pmids), digits = 2)[1] 79.66download_pmc_text <- function(pmcid,
out_dir = here::here("output/fulltexts/europe_pmc/")
) {
url_xml <- paste0("https://www.ebi.ac.uk/",
"europepmc/webservices/rest/",
pmcid,
"/fullTextXML"
)
resp <- GET(url_xml)
# MED/20708005
# ---- Fallback URL ----
if(status_code(resp) != 200){
#print(paste0("Trying alternative URL for ", pmcid))
url_xml <- paste0("https://europepmc.org/",
"oai.cgi?verb=GetRecord",
"&metadataPrefix=pmc",
"&identifier=oai:europepmc.org:",
pmcid)
resp <- GET(url_xml)
}
# ---- Fail if still bad ----
if(status_code(resp) != 200){
#message("Failed to fetch XML for ", pmcid)
return(NULL)
}
# ---- Parse XML ----
xml_content <- read_xml(
content(resp,
as = "text",
encoding = "UTF-8")
)
xml_content <- read_xml(content(resp,
as = "text",
encoding = "UTF-8")
)
article_node = xml_find_first(xml_content,
"//*[local-name() = 'article']"
)
if (is.na(article_node)) {
message("No <article> node found for ", pmcid)
return(NULL)
}
# --- Save ---
write_xml(article_node,
paste0(out_dir, pmcid, ".xml")
)
}
for(article in pmcids[pmcids != ""]){
download_pmc_text(article)
}print("Number of downloaded full text files")[1] "Number of downloaded full text files"print("From European PMC:")[1] "From European PMC:"n_euro_pmc <- length(list.files(here::here("output/fulltexts/europe_pmc/"),
pattern = "\\.xml$")
)
print("Percentage of pmids with full text from European PMC:")[1] "Percentage of pmids with full text from European PMC:"round(100 * n_euro_pmc / length(pmids), digits = 2)[1] 52.77converted_ids <-
data.table::fread(here::here("output/gwas_cat/gwas_pubmed_to_pmcid_mapping.csv")
)
convert_xml_text <- function(xml_content,
text #output text file
){
for(section in 1:xml_length(xml_content)){
section_node = xml_child(xml_content, section)
if(length(xml_path(xml_find_all(section_node,
".//*[.//title and .//p]"
)
)
) == 0
)
{
# Get section name:
section_name = xml_text(xml_find_all(section_node,
".//title"))
section_name = str_squish(section_name)
if(!rlang::is_empty(section_name)) {
text = c(text, paste0("\n\n", section_name, "\n"))
}
# Get paragraphs
para_nodes = xml_find_all(section_node, ".//p")
para_texts = xml_text(para_nodes)
para_texts = str_squish(para_texts)
if(!rlang::is_empty(para_texts)) {
text = c(text, paste0("\n",
para_texts,
"\n")
)
}
if(rlang::is_empty(section_name) &&
rlang::is_empty(para_texts)) {
all_node_text <- xml_text(section_node)
if(!rlang::is_empty(all_node_text)){
text = c(text, paste0("\n",
all_node_text,
"\n")
)
}
}
label <- xml_text(xml_find_all(section_node,
".//label"))
href <- xml_attr(xml_find_all(section_node,
".//media"),
"href")
if(!rlang::is_empty(label) && !rlang::is_empty(href)) {
text = c(text, paste0("\n", label, ". ", href, "\n"))
}
} else {
for(subsection in 1:xml_length(section_node)){
subsection_node = xml_child(section_node,
subsection
)
if(length(xml_children(subsection_node)) == 0){
if(xml_name(subsection_node) == "title"){
text = c(text,
paste0("\n\n",
xml_text(subsection_node),
"\n")
)
} else {
text = c(text,
paste0("\n",
xml_text(subsection_node),
"\n")
)
}
next
}
# Get section name:
subsection_name = xml_text(xml_find_all(subsection_node,
".//title")
)
subsection_name = str_squish(subsection_name)
if(!rlang::is_empty(subsection_name)) {
# Add spaces around section titles
text = c(text, paste0("\n\n",
subsection_name,
"\n")
)
}
# Get paragraphs
para_nodes = xml_find_all(subsection_node,
".//p")
para_texts = xml_text(para_nodes)
para_texts = str_squish(para_texts)
if(!rlang::is_empty(para_texts)) {
# Add spaces around paragraphs
text = c(text, paste0("\n",
para_texts,
"\n")
)
}
if(rlang::is_empty(subsection_name) &&
rlang::is_empty(para_texts)) {
all_node_text <- xml_text(subsection_node)
if(!rlang::is_empty(all_node_text)){
text = c(text, paste0("\n",
all_node_text,
"\n")
)
}
}
}
}
}
return(text)
}
extract_app_text <- function(xml_back,
text){
# Add separator for appendices section
text <- c(text, "\n\n=== APPENDICES ===\n")
#browser()
for(node_id in 1:xml_length(xml_back)){
node = xml_child(xml_back,
node_id)
#print(node)
if(xml_name(node) == "app-group" &
length(xml_find_all(node, ".//sec")) > 0) {
app_node = xml_find_all(node, ".//sec")
text = convert_xml_text(app_node, text)
} else if(xml_name(node) == "ref-list") {
next
} else {
text = convert_xml_text(node,
text)
}
}
download_pmc_text <- function(pmcid,
out_dir = here::here("output/fulltexts/europepmc")
) {
url_xml <- paste0("https://www.ebi.ac.uk/europepmc/webservices/rest/",
pmcid,
"/fullTextXML"
)
resp <- GET(url_xml)
if (status_code(resp) != 200) stop("Failed to fetch XML for ", pmcid)
xml_content <- read_xml(content(resp,
as = "text",
encoding = "UTF-8")
)
# Get text body xml content
#browser()
xml_body = xml_child(xml_content, "body")
xml_back = xml_child(xml_content, "back")
#browser()
# Build text file
# By converting xml structure into sections and subsections
text = c()
text = convert_xml_text(xml_body,
text
)
text = c(text, "\n\n")
text = extract_app_text(xml_back,
text
)
# if Nat Genet article
if(grepl("Nature genetics",
xml_text(xml_find_all(xml_content,
".//journal-title")),
ignore.case = TRUE
)
){
# Find all figure nodes
xml_figures <- xml_find_all(xml_content,
".//fig")
if (length(xml_figures) != 0){
text = c(text, "\n\nFigures:\n")
}
for(nodes in 1:length(xml_figures)){
figure_node = xml_figures[nodes]
# Extract label:
label <- xml_text(xml_find_all(figure_node,
".//label"))
# Extract title
title = xml_text(xml_find_all(figure_node, ".//title"))
if(!rlang::is_empty(label) | !rlang::is_empty(title)){
text = c(text,
paste0("\n", label, ". ", title, "\n")
)
}
# Extract caption
caption = xml_text(xml_find_all(figure_node,
".//caption//p"))
if(!rlang::is_empty(caption)){
text = c(text,
paste0("\n", caption, "\n")
)
}
}
}
# --- Save ---
text_full <- paste(text, collapse = " ")
txt_file <- file.path(out_dir,
paste0(pmcid, ".txt")
)
writeLines(text_full,
txt_file,
useBytes = TRUE)
#message("✅ Cleaned text saved for ", pmcid)
invisible(text_full)
}
safe_download_pmc_text <- purrr::safely(download_pmc_text)
# Download full texts for all PMCIDs
for(pmcid in pmcids){
if(pmcid != ""){
result <- safe_download_pmc_text(pmcid)
# if(!is.null(result$error)){
# message("❌ Failed to download text for ", pmcid,
# ": ", result$error)
# }
}
}
# How many texts saved?
length(list.files(here::here("output/fulltexts/europepmc"),
pattern = "\\.txt$")
)
# get list of pmcids with full text - author_manuscript available
# available in XML and plain text for text mining purposes.
aws s3 cp s3://pmc-oa-opendata/author_manuscript/txt/metadata/txt/author_manuscript.filelist.txt output/fulltexts/aws_locations/ --no-sign-request
# get list of pmcids with full text - non-commercial use
# oa_noncomm
aws s3 cp s3://pmc-oa-opendata/oa_noncomm/txt/metadata/txt/oa_noncomm.filelist.txt output/fulltexts/aws_locations/ --no-sign-request
# get list of pmcids with full text, commercial list
# oa_comm
aws s3 cp s3://pmc-oa-opendata/oa_comm/txt/metadata/txt/oa_comm.filelist.txt output/fulltexts/aws_locations/ --no-sign-request
# get list of pmcids with full text, commercial list
# oa_other
aws s3 cp s3://pmc-oa-opendata/oa_other/txt/metadata/txt/oa_other.filelist.txt output/fulltexts/aws_locations/ --no-sign-request
europeanpmc_full_texts <-
list.files(here::here("output/fulltexts/europe_pmc"),
pattern = "\\.xml"
)
# get pmcids of these files
europeanpmc_full_texts <-
gsub("\\.xml$",
"",
europeanpmc_full_texts
) left_over_pmcids = pmcids[!pmcids %in% europeanpmc_full_texts]
print("Number of remaining pmcids without full text:")[1] "Number of remaining pmcids without full text:"length(left_over_pmcids)[1] 267author_manu = data.table::fread(here::here("output/fulltexts/aws_locations/author_manuscript.filelist.txt"))
oa_noncomm = data.table::fread(here::here("output/fulltexts/aws_locations/oa_noncomm.filelist.txt"))
oa_comm = data.table::fread(here::here("output/fulltexts/aws_locations/oa_comm.filelist.txt"))
author_manu_to_get <-
author_manu |>
dplyr::filter(AccessionID %in% left_over_pmcids)
print("Number of papers to download in Author Manuscripts section:")[1] "Number of papers to download in Author Manuscripts section:"nrow(author_manu_to_get)[1] 160oa_noncomm_to_get =
oa_noncomm |>
# dplyr::filter(PMID %in% names(left_over_pmcids))
dplyr::filter(AccessionID %in% left_over_pmcids)
oa_comm_to_get =
oa_comm |>
# dplyr::filter(PMID %in% names(left_over_pmcids))
dplyr::filter(AccessionID %in% left_over_pmcids)
print("Number of papers to download in Open Access PMC section:")[1] "Number of papers to download in Open Access PMC section:"nrow(oa_noncomm_to_get) + nrow(oa_comm_to_get)[1] 1oa_noncomm_to_get <-
oa_noncomm_to_get |>
dplyr::filter(!c(AccessionID %in% author_manu_to_get$AccessionID))
oa_ncomm_to_get <-
oa_noncomm_to_get |>
dplyr::filter(!c(AccessionID %in% author_manu_to_get$AccessionID))
not_available = left_over_pmcids[!c(left_over_pmcids %in%
c(oa_noncomm_to_get$AccessionID,
oa_comm_to_get$AccessionID,
author_manu_to_get$AccessionID)
)]
print("Number of papers without full text available in NCBI Cloud Service:")[1] "Number of papers without full text available in NCBI Cloud Service:"length(not_available)[1] 106file_paths =
c(oa_noncomm_to_get$Key,
oa_comm_to_get$Key,
author_manu_to_get$Key)
file_paths <- str_replace_all(file_paths,
pattern = "txt",
replacement = "xml")
# percentage not available, from all papers
100 * length(not_available) / length(pmids)[1] 10.67472writeLines(
file_paths,
here::here("output/fulltexts/aws_locations/selected_paths.txt")
)
system(
paste(
"xargs -I {} aws s3 cp",
"s3://pmc-oa-opendata/{}",
shQuote(here::here("output/fulltexts/ncbi_cloud/")),
"--no-sign-request",
"<",
shQuote(here::here("output/fulltexts/aws_locations/selected_paths.txt"))
)
)# old getting dois:
entrez_info <-
entrez_summary(db="pubmed",
id=not_convertable_pmids)
dois <-
entrez_info |>
purrr::map(function(x) {
x$articleids |>
filter(idtype == "doi") |>
pull(value)
}
)library(openalexR)openalexR v2.0.0 introduces breaking changes.
See NEWS.md for details.
To suppress this message, add `openalexR.message = suppressed` to your .Renviron file.convert_pmid_df <- fread(here::here("data/europe_pmc/PMID_PMCID_DOI.csv"))Warning in fread(here::here("data/europe_pmc/PMID_PMCID_DOI.csv")): Found and
resolved improper quoting out-of-sample. First healed line 8637909:
<<17234576,PMC2742408,"https://doi.org/10.1102/1470-7330.2007.0001>>. If the
fields are not quoted (e.g. field separator does not appear within any field),
try quote="" to avoid this warning.not_convertable_pmids <- converted_ids |>
filter(pmcids == "") |>
pull(PMID)
doi_information <-
convert_pmid_df |>
filter(PMID %in% not_convertable_pmids)
doi_information |>
filter(DOI == "")Empty data.table (0 rows and 3 cols): PMID,PMCID,DOIdoi_information$PMID |> unique() |> length()[1] 202length(not_convertable_pmids)[1] 202# get open alex works for pmids
open_alex_works <- oa_fetch(
doi = unique(doi_information$DOI),
entity = "works",
options = list(select = c("doi",
"open_access"))
)
# no best open access location:
open_alex_works |>
filter(is.na(oa_url)) |>
nrow()[1] 110# pdf link available:
open_alex_works |>
filter(grepl("pdf", oa_url)) |>
nrow()[1] 65to_download_pdfs <-
open_alex_works |>
filter(grepl(".pdf", oa_url)) |>
pull(oa_url)
writeLines(
to_download_pdfs,
here::here("output/fulltexts/pdfs/pdf_links_to_download.txt"))
cd output/fulltexts/pdfs
while read -r url; do
curl -O "$url"
done < pdf_links_to_download.txt
# not_available
not_convertable_pmids <- converted_ids |>
filter(pmcids == "") |>
pull(PMID)
all_tgz_links = c()
for(article_id in "PMC2613843"){
url <- paste0("https://www.ncbi.nlm.nih.gov/pmc/utils/oa/oa.fcgi?id=",
article_id)
resp <- GET(url)
xml_data <- xml_child(content(resp), "records")
tgz_link <- xml_find_first(xml_data,
".//link[@format='tgz']/@href")
tgz_link <- xml_text(tgz_link)
if (is.na(tgz_link)) {
print("No tar.gz link found.")
} else {
all_tgz_links <- append(all_tgz_links,
tgz_link)
}
}
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.7.3
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 data.table_1.17.8 dplyr_1.1.4 here_1.0.1
[5] stringr_1.6.0 xml2_1.4.0 httr_1.4.7 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] jsonlite_2.0.0 compiler_4.3.1 BiocManager_1.30.26
[4] renv_1.0.3 promises_1.3.3 tidyselect_1.2.1
[7] Rcpp_1.1.0 git2r_0.36.2 callr_3.7.6
[10] later_1.4.4 jquerylib_0.1.4 yaml_2.3.10
[13] fastmap_1.2.0 R6_2.6.1 generics_0.1.4
[16] curl_7.0.0 knitr_1.50 tibble_3.3.0
[19] rprojroot_2.1.0 bslib_0.9.0 pillar_1.11.1
[22] rlang_1.1.6 cachem_1.1.0 stringi_1.8.7
[25] httpuv_1.6.16 xfun_0.55 getPass_0.2-4
[28] fs_1.6.6 sass_0.4.10 cli_3.6.5
[31] withr_3.0.2 magrittr_2.0.4 ps_1.9.1
[34] digest_0.6.37 processx_3.8.6 rstudioapi_0.17.1
[37] lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.5
[40] glue_1.8.0 whisker_0.4.1 rmarkdown_2.30
[43] tools_4.3.1 pkgconfig_2.0.3 htmltools_0.5.8.1