epmc_search: Search Europe PMC publication database

Description

This is the main function to search Europe PMC RESTful Web Service (http://europepmc.org/RestfulWebService)

Usage

1
2
epmc_search(query = NULL, output = "parsed", synonym = FALSE,
  verbose = TRUE, limit = 100, sort = NULL)

Arguments

query

character, search query. For more information on how to build a search query, see http://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. Disabled by default.

verbose

logical, print some information on what is going on.

limit

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

sort

character, sort results by order (asc, desc) and sort field (e.g. CITED, P_PDATE), seperated with a blank. For example, sort results by times cited in descending order: sort = 'CITED desc'.

Value

tibble

See Also

http://europepmc.org/Help

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
## Not run: 
#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)

# include mesh and uniprot synonyms in search
my.data <- epmc_search(query = 'aspirin', synonym = TRUE)

# get 100 most cited atricles from PLOS ONE
epmc_search(query = 'ISSN:	1932-6203', sort = 'CITED desc')

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

# change output


## End(Not run)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.