Europe PMC utilities

Share:

Description

Europe PMC utilities

Usage

1
2
3
4
5
6
eupmc_search(query, resulttype = NULL, synonym = FALSE, per_page = 25,
  page = 1, ...)

eupmc_fields(...)

eupmc_xml(id, ...)

Arguments

query

(character) Search terms. Required.

resulttype

(character) The result type can either be idlist, core or lite. This parameter determines the fields returned by XML and JSON formats, but it has no effect on the DC format. See Details.

synonym

(boolean) Synonym searches are not made by default (Default: FALSE), however queries can be expanded using MeSH terminology and the UniProt synonyms list. For example aspirin, a synonym would be acetylsalicylic acid;this could be included in the search by setting the parameter value to TRUE

per_page

(integer) Number of records to return. Max: 1000. Default: 25

page

Page (integer) Page numbers start at 1. Default: 1

...

Further args passed on to GET

id

A single Europe PMC article identifier, begins with "PMC", followed by numbers, e.g., "PMC3257301"

Details

resulttype parameter options:

  • idlist - returns a list of IDs and sources for the given search terms

  • lite - returns key metadata for the given search terms; this is the default value if the parameter is unspecified.

  • core - returns full metadata for a given publication ID; including abstract, full text links, and MeSH terms.

Value

eupmc_search returns a list with results. eupmc_fields returns a data.frame. eupmc_xml returns an object of class xml_document

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
## Not run: 
# search
eupmc_search(query = 'ecology')
eupmc_search(query = 'human malaria')
eupmc_search(query = '"human malaria"')
eupmc_search(query = 'auth:stoehr')
eupmc_search(query = 'journal:pnas')
eupmc_search(query = 'journal:pnas')
eupmc_search(query = 'ext_id:781840 src:med')
eupmc_search(query = 'ext_id:IND43783977 src:agr')

# list indexed search fields
head(eupmc_fields())

# get full text XML
eupmc_xml('PMC3257301')

## End(Not run)