Last updated: 2026-01-12
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genomics_ancest_disease_dispar/
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Ignored: .DS_Store
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Ignored: analysis/.DS_Store
Ignored: ancestry_dispar_env/
Ignored: data/.DS_Store
Ignored: data/RCDCFundingSummary_01042026.xlsx
Ignored: data/cdc/
Ignored: data/cohort/
Ignored: data/epmc/
Ignored: data/europe_pmc/
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Ignored: data/gbd/IHME-GBD_2021_DATA-d8cf695e-1.csv
Ignored: data/gbd/IHME-GBD_2023_DATA-73cc01fd-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/2025AA/
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Ignored: data/icd/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5e2c27f | IJbeasley | 2026-01-12 | Update steps for downloading abstracts |
| html | bbd5e28 | IJbeasley | 2025-12-29 | Build site. |
| Rmd | ed0795e | IJbeasley | 2025-12-29 | Add getting abstracts as an extra step |
library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlibrary(rentrez)## 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 <- data.table::fread(here::here("output/icd_map/gwas_disease_to_icd10_mapping.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 <-
gwas_study_info |>
#filter(COHORT != "") |>
select(PUBMED_ID) |>
distinct()
pmids = gwas_study_info$PUBMED_ID
print("Number of unique pubmed ids for disease studies:")[1] "Number of unique pubmed ids for disease studies:"pmids |> length()[1] 4576set_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)
missing_abstracts <- pmids[abstracts == "MISSING"]
print("Number of missing abstracts:")
length(missing_abstracts)
# Remove missing abstracts
pmids <- pmids[abstracts != "MISSING"]
abstracts <- abstracts[abstracts != "MISSING"]
print("Number of abstracts retrieved:")
length(abstracts)
# 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)
}
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] rentrez_1.2.4 dplyr_1.1.4 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 stringr_1.6.0 git2r_0.36.2
[10] callr_3.7.6 later_1.4.4 jquerylib_0.1.4
[13] yaml_2.3.10 fastmap_1.2.0 here_1.0.1
[16] R6_2.6.1 generics_0.1.4 knitr_1.50
[19] XML_3.99-0.19 tibble_3.3.0 rprojroot_2.1.0
[22] bslib_0.9.0 pillar_1.11.1 rlang_1.1.6
[25] cachem_1.1.0 stringi_1.8.7 httpuv_1.6.16
[28] xfun_0.55 getPass_0.2-4 fs_1.6.6
[31] sass_0.4.10 cli_3.6.5 withr_3.0.2
[34] magrittr_2.0.4 ps_1.9.1 digest_0.6.37
[37] processx_3.8.6 rstudioapi_0.17.1 lifecycle_1.0.4
[40] vctrs_0.6.5 data.table_1.17.8 evaluate_1.0.5
[43] glue_1.8.0 whisker_0.4.1 rmarkdown_2.30
[46] httr_1.4.7 tools_4.3.1 pkgconfig_2.0.3
[49] htmltools_0.5.8.1