Question: R script to download all abstracts of Nature in 2020 from Pubmed
0
gravatar for Shicheng Guo
6 weeks ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Dear All,

Anyone can share a R command to download all abstracts of Nature in 2020 from Pubmed

Thanks.

pubmed abstract • 176 views
ADD COMMENTlink modified 5 weeks ago • written 6 weeks ago by Shicheng Guo8.3k
1

You might wish to have a look at this tool. See the end of the webpage for examples.

ADD REPLYlink written 6 weeks ago by Sishuo Wang200
3
gravatar for Alex Nesmelov
6 weeks ago by
Alex Nesmelov110
Alex Nesmelov110 wrote:
library(rentrez)

paper_ids <- entrez_search(db = "pubmed",
            "Nature[jour] AND 2020[dp]",
            retmax = 9999,
            use_history = T)

raw_abs <- entrez_fetch(db="pubmed",
                    web_history = paper_ids$web_history,
                    rettype="abstract")
ADD COMMENTlink written 6 weeks ago by Alex Nesmelov110
1
gravatar for Shicheng Guo
5 weeks ago by
Shicheng Guo8.3k
Shicheng Guo8.3k wrote:

Find another way as good as @Alex Nesmelov's proposal. Thanks Alex Nesmelov!

library(easyPubMed)
my_query <- 'Damiano Fantini[AU] AND "2018"[PDAT]'
my_entrez_id <- get_pubmed_ids(my_query)
my_abstracts_txt <- fetch_pubmed_data(my_entrez_id, format = "abstract")
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Shicheng Guo8.3k

You should consider accepting @Alex's answer in that case, since it must work and it gave you the direction to find your own.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax87k
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