eupmc: Europe PMC utilities

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Description

Europe PMC utilities

Usage

eupmc_search(
  query,
  resulttype = "lite",
  synonym = FALSE,
  per_page = 25,
  cursorMark = "*",
  ...
)

eupmc_fields(...)

eupmc_xml(id, ...)

Arguments

query	(character) Search terms. Required. See Details
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
cursorMark	(character) cursor string, default: *
...	curl options passed on to crul::HttpClient
id	A single Europe PMC article identifier, begins with "PMC", followed by numbers, e.g., "PMC3257301"
sort	(character) The default sort order is relevance. Specify the sort field and sort order. This parameter provides "asc" or "desc" order for every single-valued field: P_PDATE_D, AUTH_FIRST, CITED etc. For example sorting by CITED in ascending order: CITED asc

Value

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

query parameter options

• a keyword or combination of keywords (e.g. HPV virus).

• a phrase with enclosing speech marks (e.g. "human malaria").

• a fielded search (e.g. auth:stoehr). Available search fields are listed in the Appendix 1 of the Reference Guide or can be retrieved using the fields module of the API.

• a specific publication (e.g. ext_id:781840 src:med) Specify ext_id as the article identifier, and src as the source database. List of the data sources can be found on the help pages or in section 3 of the Reference Guide.

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.

References

https://europepmc.org/RestfulWebService

Examples

## 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
x <- eupmc_fields()
NROW(x)
head(x)

# get full text XML
eupmc_xml('PMC3257301')

## End(Not run)

fulltext documentation built on June 12, 2021, 9:06 a.m.