europepmc - an R client for the Europe PMC RESTful article API

Description

What is europepmc?:

europepmc facilitates access to Europe PMC RESTful Web Service. Europe PMC covers life science literature and gives access to open access full texts. Coverage is not only restricted to Europe, but articles and abstracts are indexed from all over the world. Europe PMC ingests all PubMed content and extends its index with other sources, including Agricola, a bibliographic database of citations to the agricultural literature, or Biological Patents.

Besides searching abstracts and full text, europepmc can be used to retrieve reference sections and citations, text-mined terms or cross-links to other databases hosted by the European Bioinformatics Institute (EBI).

For more information about Europe PMC, see their current paper: Ferguson, C., Araújo, D., Faulk, L., Gou, Y., Hamelers, A., Huang, Z., Ide-Smith, M., Levchenko, M., Marinos, N., Nambiar, R., Nassar, M., Parkin, M., Pi, X., Rahman, F., Rogers, F., Roochun, Y., Saha, S., Selim, M., Shafique, Z., … McEntyre, J. (2020). Europe PMC in 2020. Nucleic Acids Research, 49(D1), D1507–D1514. doi:10.1093/nar/gkaa994.

Author(s)

Maintainer: Najko Jahn najko.jahn@gmail.com [copyright holder]

Other contributors:

• Maëlle Salmon [contributor]

See Also

Useful links:

• https://docs.ropensci.org/europepmc/

• https://github.com/ropensci/europepmc/

• Report bugs at https://github.com/ropensci/europepmc/issues

Get annotations by article

Description

Retrieve text-mined annotations contained in abstracts and open access full-text articles.

Usage

epmc_annotations_by_id(ids = NULL)

Arguments

Value

returns text-mined annotations in a tidy format with the following variables

source

Publication data source

ext_id

Article Identifier

pmcid

PMCID that locates full-text in Pubmed Central

prefix

Text snipped found before the annotation

exact

Annotated entity

postfix

Text snipped found after the annotation

name

Targeted entity

uri

Uniform link dictionary entry for targeted entity

id

URL to full-text occurence of the annotation

type

Type of annotation like Chemicals

section

Article section mentioning the annotation like Methods

provider

Annotation data provider

subtype

Sub-data provider

Examples

## Not run: 
  annotations_by_id("MED:28585529")
  # multiple ids
  annotations_by_id(c("MED:28585529", "PMC:PMC1664601"))

## End(Not run)

Get citations for a given publication

Description

Finds works that cite a given publication.

Usage

epmc_citations(ext_id = NULL, data_src = "med", limit = 100, verbose = TRUE)

Arguments

Value

Metadata of citing documents as data.frame

Examples

## Not run: 
epmc_citations("PMC3166943", data_src = "pmc")
epmc_citations("9338777")

## End(Not run)

Retrieve external database entities referenced in a given publication

Description

This function returns EBI database entities referenced in a publication from Europe PMC RESTful Web Service.

Usage

epmc_db(
  ext_id = NULL,
  data_src = "med",
  db = NULL,
  limit = 100,
  verbose = TRUE
)

Arguments

Value

Cross-references as data.frame

Examples

  ## Not run: 
  epmc_db("12368864", db = "uniprot", limit = 150)
  epmc_db("25249410", db = "embl")
  epmc_db("14756321", db = "uniprot")
  epmc_db("11805837", db = "pride")
  
## End(Not run)

Retrieve the number of database links from Europe PMC publication database

Description

This function returns the number of EBI database links associated with a publication.

Usage

epmc_db_count(ext_id = NULL, data_src = "med")

Arguments

Details

Europe PMC supports cross-references between literature and the following databases:

'ARXPR'

Array Express, a database of functional genomics experiments

'CHEBI'

a database and ontology of chemical entities of biological interest

'CHEMBL'

a database of bioactive drug-like small molecules

'EMBL'

now ENA, provides a comprehensive record of the world's nucleotide sequencing information

'INTACT'

provides a freely available, open source database system and analysis tools for molecular interaction data

'INTERPRO'

provides functional analysis of proteins by classifying them into families and predicting domains and important sites

'OMIM'

a comprehensive and authoritative compendium of human genes and genetic phenotypes

'PDB'

European resource for the collection, organisation and dissemination of data on biological macromolecular structures

'UNIPROT'

comprehensive and freely accessible resource of protein sequence and functional information

'PRIDE'

PRIDE Archive - proteomics data repository

Value

data.frame with counts for each database

Examples

  ## Not run: 
  epmc_db_count(ext_id = "10779411")
  epmc_db_count(ext_id = "PMC3245140", data_src = "PMC")
  
## End(Not run)

Get details for individual records

Description

This function returns parsed metadata for a given publication ID including abstract, full text links, author details including ORCID and affiliation, MeSH terms, chemicals, grants.

Usage

epmc_details(ext_id = NULL, data_src = "med")

Arguments

Value

list of data frames

Examples

## Not run: 
epmc_details(ext_id = "26980001")
epmc_details(ext_id = "24270414")

# PMC record
epmc_details(ext_id = "PMC4747116", data_src = "pmc")

# Other sources:
# Agricolo
epmc_details("IND43783977", data_src = "agr")
# Biological Patents
epmc_details("EP2412369", data_src = "pat")
# Chinese Biological Abstracts
epmc_details("583843", data_src = "cba")
# CiteXplore
epmc_details("C6802", data_src = "ctx")
# NHS Evidence
epmc_details("338638", data_src = "hir")
# Theses
epmc_details("409323", data_src = "eth")
# Preprint
epmc_details("PPR158112", data_src = "ppr")

## End(Not run)

Fetch Europe PMC full texts

Description

This function loads full texts into R. Full texts are in XML format and are only provided for the Open Access subset of Europe PMC.

Usage

epmc_ftxt(ext_id = NULL)

Arguments

Value

xml_document

Examples

  ## Not run: 
  epmc_ftxt("PMC3257301")
  epmc_ftxt("PMC3639880")
  
## End(Not run)

Fetch Europe PMC books

Description

Use this function to retrieve book XML formatted full text for the Open Access subset of the Europe PMC bookshelf.

Usage

epmc_ftxt_book(ext_id = NULL)

Arguments

Value

xml_document

Examples

  ## Not run: 
  epmc_ftxt_book("NBK32884")
  
## End(Not run)

Get search result count

Description

Search over Europe PMC and retrieve the number of results found

Usage

epmc_hits(query = NULL, ...)

Arguments

See Also

epmc_search

Examples

 ## Not run: 
 epmc_hits('abstract:"burkholderia pseudomallei"')
 epmc_hits('AUTHORID:"0000-0002-7635-3473"')
 
## End(Not run)

Get the yearly number of hits for a query and the total yearly number of hits for a given period

Description

Get the yearly number of hits for a query and the total yearly number of hits for a given period

Usage

epmc_hits_trend(query, synonym = TRUE, data_src = "med", period = 1975:2016)

Arguments

Details

A similar function was used in https://masalmon.eu/2017/05/14/evergreenreviewgraph/ where it was advised to not plot no. of hits over time for a query, but to normalize it by the total no. of hits.

Value

a data.frame (dplyr tbl_df) with year, total number of hits (all_hits) and number of hits for the query (query_hits)

Examples

## Not run: 
# aspirin as query
epmc_hits_trend('aspirin', period = 2006:2016, synonym = FALSE)
# link to cran packages in reference lists
epmc_hits_trend('REF:"cran.r-project.org*"', period = 2006:2016, synonym = FALSE)
# more complex with publication type review
epmc_hits_trend('(REF:"cran.r-project.org*") AND (PUB_TYPE:"Review" OR PUB_TYPE:"review-article")',
period = 2006:2016, synonym = FALSE)

## End(Not run)

Get links to external sources

Description

With the External Link services, Europe PMC allows third parties to publish links from Europe PMC to other webpages or tools. Current External Link providers, which can be selected through Europe PMC's advanced search, include Wikipedia, Dryad Digital Repository or other open services. For more information, see https://europepmc.org/labslink.

Usage

epmc_lablinks(
  ext_id = NULL,
  data_src = "med",
  lab_id = NULL,
  limit = 100,
  verbose = TRUE
)

Arguments

Value

Links found as nested data_frame

Examples

  ## Not run: 
  # Fetch links
  epmc_lablinks("24007304")
  # Link to Altmetric (lab_id = "1562")
  epmc_lablinks("25389392", lab_id = "1562")

  # Links to Wikipedia
  epmc_lablinks("24007304", lab_id = "1507")

  # Link to full text copy archived through the institutional repo of
  Bielefeld University
  epmc_lablinks("12736239", lab_id = "1056")
  
## End(Not run)

Summarise links to external sources

Description

With the External Link services, Europe PMC allows third parties to publish links from Europe PMC to other webpages or tools. Current External Link providers, which can be selected through Europe PMC's advanced search, include Wikipedia, Dryad Digital Repository or the institutional repo of Bielefeld University. For more information, see https://europepmc.org/labslink.

Usage

epmc_lablinks_count(ext_id = NULL, data_src = "med")

Arguments

Value

data.frame with counts for each database

Examples

   ## Not run: 
   epmc_lablinks_count("24023770")
   epmc_lablinks_count("PMC3986813", data_src = "pmc")
   
## End(Not run)

Obtain a summary of hit counts

Description

This functions returns the number of results found for your query, and breaks it down to the various publication types, data sources, and subsets Europe PMC provides.

Usage

epmc_profile(query = NULL, synonym = TRUE)

Arguments

Examples

## Not run: 
  epmc_profile('malaria')
  # use field search, e.g. query materials and reference section for
  # mentions of "ropensci"
  epmc_profile('(METHODS:"ropensci")')
 
## End(Not run)

Get references for a given publication

Description

This function retrieves all the works listed in the bibliography of a given article.

Usage

epmc_refs(ext_id = NULL, data_src = "med", limit = 100, verbose = TRUE)

Arguments

Value

returns reference section as tibble

Examples

## Not run: 
epmc_refs("PMC3166943", data_src = "pmc")
epmc_refs("25378340")
epmc_refs("21753913")

## End(Not run)

Search Europe PMC publication database

Description

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

Value

tibble

See Also

https://europepmc.org/Help

Examples

## 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)

# 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


## End(Not run)

Get one page of results when searching Europe PubMed Central

Description

In general, use epmc_search instead. It calls this function, calling all pages within the defined limit.

Usage

epmc_search_(
  query = NULL,
  limit = 100,
  output = "parsed",
  page_token = NULL,
  ...
)

Arguments

See Also

epmc_search

Search Europe PMC by DOIs

Description

Look up DOIs indexed in Europe PMC and get metadata back.

Usage

epmc_search_by_doi(doi = NULL, output = "parsed")

Arguments

Examples

## Not run: 
# single DOI name
epmc_search_by_doi(doi = "10.1161/strokeaha.117.018077")
# multiple DOIname in a vector
my_dois <- c(
  "10.1159/000479962",
  "10.1002/sctm.17-0081",
  "10.1161/strokeaha.117.018077",
  "10.1007/s12017-017-8447-9")
epmc_search_by_doi(doi = my_dois)
# full metadata
epmc_search_by_doi(doi = my_dois, output = "raw")

## End(Not run)

Search Europe PMC by a DOI name

Description

Please use epmc_search_by_doi instead. It calls this method, returning open access status information from all your requests.

Usage

epmc_search_by_doi_(doi, .pb = NULL, output = NULL)

Arguments

Examples

## Not run: 
  epmc_search_by_doi_("10.1159/000479962")

## End(Not run)