In pachterlab/museumst: Museum of Spatial Transcriptomics

knitr::opts_chunk$set(echo = TRUE)

Again, since there aren't many papers from arXiv and it isn't straightforward to get the abstract from the title of doi, I'll do the arXiv ones manually.

library(tidyverse)
library(easyPubMed)
library(rbiorxiv)
library(lubridate)
theme_set(theme_bw())

nms <- c("Prequel", "Microdissection", "smFISH", "Array", "ISS", "No imaging", 
         "Analysis", "Prequel analysis")
all_sheets <- read_metadata(sheet_use = nms, update = TRUE)

abstracts <- readRDS("curated_abstracts.rds")

abstracts <- abstracts %>% 
  filter(pmid != "32619996" | is.na(pmid))

pmids <- unique(all_sheets$pmid)
pmids_old <- unique(abstracts$pmid)
pmids <- pmids[!is.na(pmids)]
pmids_old <- pmids_old[!is.na(pmids_old)]

pmids_new <- setdiff(pmids, pmids_old)
pmid_res <- map(pmids_new, slowly(get_pubmed_ids, rate_delay(0.2)), 
                api_key = Sys.getenv("PUBMED_API_KEY"))
my_xmls <- map(pmid_res, fetch_pubmed_data)
xmls_list <- map(my_xmls, articles_to_list)
abstracts_new <- map_dfr(xmls_list, article_to_df, getAuthors = FALSE, max_chars = 1e6)

Also get new abstracts from bioRxiv

for_biorxiv <- all_sheets %>% 
  filter(journal == "bioRxiv") %>% 
  anti_join(abstracts, by = "title") %>% 
  mutate(doi = str_remove(URL, "^https://doi.org/"))
for_biorxiv

for_biorxiv <- for_biorxiv %>% 
  mutate(abstract = map_chr(doi, ~ slowly(biorxiv_content, rate_delay(1))(doi = .x)[[1]]$abstract))

setdiff(names(abstracts), names(abstracts_new))

for_biorxiv <- for_biorxiv %>% 
  mutate(date_num = as.numeric(date_published)) %>% 
  unite(col = "city2", city, country, sep = ", ", remove = FALSE)

abstracts_new <- abstracts_new %>% 
  unite(col = "date_published", year, month, day, sep = "-") %>% 
  mutate(date_published = ymd(date_published),
         date_num = as.numeric(date_published)) %>% 
  select(-doi, -jabbrv)
all_sheets$pmid <- as.character(all_sheets$pmid)
abstracts_new <- abstracts_new %>% 
  left_join(all_sheets[, c("pmid", "country", "state/province", "city", "institution", "sheet")],
            by = "pmid")
abstracts_new <- abstracts_new %>% 
  unite(col = "city2", city, country, sep = ", ", remove = FALSE)

abstracts <- rbind(abstracts, abstracts_new[, names(abstracts)], for_biorxiv[, names(abstracts)])

abstracts <- abstracts %>% 
  distinct()

abstracts[duplicated(abstracts$title),]

saveRDS(abstracts, "curated_abstracts.rds")

pachterlab/museumst documentation built on April 20, 2024, 11:26 p.m.