fulltext (version 2.0)

ft_abstract: Get abstracts

Description

Get abstracts

Usage

ft_abstract(
  x,
  from = "crossref",
  plosopts = list(),
  scopusopts = list(),
  maopts = list(),
  crossrefopts = list(),
  ...
)
ft_abstract_ls()

Arguments

x

(character) DOIs as a character vector. See Details.

from

Source to query. One or more of crossref (default), plos, scopus, microsoft, or semanticscholar

plosopts

PLOS options, a named list.

scopusopts

Scopus options, a named list.

maopts

Microsoft Academic options, a named list.

crossrefopts

Crossref options, a named list.

...

curl options passed on to crul::HttpClient, see examples below

Value

An object of class ft_abstract

Details

See Rate Limits and Authentication in fulltext-package for rate limiting and authentication information, respectively. In particular take int account Semantic Scholar rate limits because we do asynchronous requests to Semantic Scholar, which means you can get data fast, but you'll hit your rate limit fast too.

There's no options to pass on when from="semanticscholar", other than curl options via ...

When from="semanticscholar", ids passed to x can be various types: DOI, S2 paper id (Semantic Scholar id), arXiv id, MAG id, ACL id, PubMed id, or Corpus id. If you use DOIs or S2 paper ids you can pass them to x as is. However, if you use other id types you need to prefix each id with the name of the type of id, options are: "arXiv", "MAG", "ACL", "PMID", "CorpusID"

Examples

# NOT RUN {
# List publishers included
ft_abstract_ls()

# }
# NOT RUN {
# PLOS
## search
(res <- ft_search(query = 'biology', from = 'plos', limit = 25,
   plosopts = list(fq = list('doc_type:full', '-article_type:correction',
                  '-article_type:viewpoints'))))
## get abstracts
dois <- res$plos$data$id
(out <- ft_abstract(x = dois, from = "plos"))
out$plos

# Semantic Scholar
(out <- ft_abstract(x = dois, from = "semanticscholar"))
out$semanticscholar
## using arxiv ids
arxiv_ids <- c("0710.3491", "0804.0713", "0810.4821", "1003.0315")
(out <- ft_abstract(x = paste0("arXiv:", arxiv_ids), from = "semanticscholar"))
out$semanticscholar

# Scopus
opts <- list(key = Sys.getenv('ELSEVIER_SCOPUS_KEY'))

## search
(res <- ft_search(query = 'biology', from = 'scopus', scopusopts = opts,
  limit = 25))
## get abstract
dois <- na.omit(res$scopus$data$`prism:doi`)
out <- ft_abstract(x = dois[1:3], from = "scopus", scopusopts = opts)
out
out$scopus

# use scopus Ids
(res <- ft_search(query = 'biology', from = 'scopus', scopusopts = opts,
  limit = 50))
ids <- fulltext:::strextract(res$scopus$data$`dc:identifier`, "[0-9]+")
(out <- ft_abstract(x = ids[1:4], from = 'scopus',
  scopusopts = list(
    key = Sys.getenv('ELSEVIER_SCOPUS_KEY'),
    id_type = "scopus_id"
  )
))

# Microsoft
key <- Sys.getenv("MICROSOFT_ACADEMIC_KEY")
(res <- ft_search("Y=[2010, 2012)", from = "microsoft",
  maopts = list(key = key)))
ids <- res$ma$data$Id
(out <- ft_abstract(x = ids, from = "microsoft",
  maopts = list(
    key = Sys.getenv('MICROSOFT_ACADEMIC_KEY')
  )
))
out$ma
cat(unlist(lapply(out$ma, "[[", "abstract")), sep = "\n\n")

# Crossref
(res <- ft_search("ecology", from = "crossref",
  crossrefopts = list(filter = c(has_abstract = TRUE))))
ids <- res$crossref$data$doi
(out <- ft_abstract(x = ids, from = "crossref"))
out$crossref

# curl options
ft_abstract("10.2458/v17i1.21696", from = "crossref", verbose = TRUE)
ft_abstract("10.1371/journal.pcbi.1002487", from = "plos", verbose = TRUE)
# }