Skip to contents

Search Europe PMC publication database

Source: R/epmc_search.r
epmc_search.Rd

This is the main function to search Europe PMC RESTful Web Service (https://europepmc.org/RestfulWebService). It fully supports the comprehensive Europe PMC query language. Simply copy & paste your query terms to R. To get familiar with the Europe PMC query syntax, check the Advanced Search Query Builder https://europepmc.org/advancesearch.

Usage

epmc_search(
  query = NULL,
  output = "parsed",
  synonym = TRUE,
  verbose = TRUE,
  limit = 100,
  sort = NULL
)

Arguments

query

character, search query. For more information on how to build a search query, see https://europepmc.org/Help

output

character, what kind of output should be returned. One of 'parsed', 'id_list' or 'raw' As default, parsed key metadata will be returned as data.frame. 'id_list' returns a list of IDs and sources. Use 'raw' to get full metadata as list. Please be aware that these lists can become very large.

synonym

logical, synonym search. If TRUE, synonym terms from MeSH terminology and the UniProt synonym list are queried, too. In order to replicate results from the website, with the Rest API you need to turn synonyms ON!

verbose

logical, print progress bar. Activated by default.

limit

integer, limit the number of records you wish to retrieve. By default, 100 are returned.

sort

character, relevance ranking is used by default. Use sort = 'cited' for sorting by the number of citations, or sort = 'date' by the most recent publications.

Value

tibble

See also

https://europepmc.org/Help

Examples

if (FALSE) { # \dontrun{
#Search articles for 'Gabi-Kat'
my.data <- epmc_search(query='Gabi-Kat')

#Get article metadata by DOI
my.data <- epmc_search(query = 'DOI:10.1007/bf00197367')

#Get article metadata by PubMed ID (PMID)
my.data <- epmc_search(query = 'EXT_ID:22246381')

#Get only PLOS Genetics article with EMBL database references
my.data <- epmc_search(query = 'ISSN:1553-7404 HAS_EMBL:y')
#Limit search to 250 PLOS Genetics articles
my.data <- epmc_search(query = 'ISSN:1553-7404', limit = 250)

# exclude MeSH synonyms in search
my.data <- epmc_search(query = 'aspirin', synonym = FALSE)

# get 100 most cited atricles from PLOS ONE publsihed in 2014
epmc_search(query = '(ISSN:1932-6203) AND FIRST_PDATE:2014', sort = 'cited')

# print number of records found
attr(my.data, "hit_count")

# change output

} # }