europepmc - R Interface to Europe PMC RESTful Web Service

europepmc facilitates access to the Europe PMC RESTful Web Service. The client furthermore supports the Europe PMC Annotations API to retrieve text-mined concepts and terms per article.

Europe PMC covers life science literature and gives access to open access full texts. Europe PMC ingests all PubMed content and extends its index with other literature and patent sources.

For more infos on Europe PMC, see:

https://europepmc.org/About

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. https://doi.org/10.1093/nar/gkaa994.

Implemented API methods

This client supports the following API methods from the Articles RESTful API:

API-Method	Description	R functions
search	Search Europe PMC and get detailed metadata	`epmc_search()`, `epmc_details()`, `epmc_search_by_doi()`
profile	Obtain a summary of hit counts for several Europe PMC databases	`epmc_profile()`
citations	Load metadata representing citing articles for a given publication	`epmc_citations()`
references	Retrieve the reference section of a publication	`epmc_refs()`
databaseLinks	Get links to biological databases such as UniProt or ENA	`epmc_db()`, `epmc_db_count()`
labslinks	Access links to Europe PMC provided by third parties	`epmc_lablinks()`, `epmc_lablinks_count()`
fullTextXML	Fetch full-texts deposited in PMC	`epmc_ftxt()`
bookXML	retrieve book XML formatted full text for the Open Access subset of the Europe PMC bookshelf	`epmc_ftxt_book()`

From the Europe PMC Annotations API:

API-Method	Description	R functions
annotationsByArticleIds	Get the annotations contained in the list of articles specified	`epmc_annotations_by_id()`

Installation

From CRAN

install.packages("europepmc")

The latest development version can be installed using the remotes package:

require(remotes)
install_github("ropensci/europepmc")

Loading into R

library(europepmc)

Search Europe PMC

The search covers both metadata (e.g. abstracts or title) and full texts. To build your query, please refer to the comprehensive guidance on how to search Europe PMC: https://europepmc.org/help. Provide your query in the Europe PMC search syntax to epmc_search().

europepmc::epmc_search(query = '"2019-nCoV" OR "2019nCoV"')
#> # A tibble: 100 × 29
#>    id        source pmid     pmcid doi   title authorString journalTitle issue journalVolume
#>    <chr>     <chr>  <chr>    <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 36754560  MED    36754560 PMC9… 10.1… Inno… Yerlikaya S… BMJ Open     2     13           
#>  2 37400836  MED    37400836 PMC1… 10.1… Effe… Ebrahimi T,… BMC Oral He… 1     23           
#>  3 37223279  MED    37223279 PMC1… 10.1… Bill… Lamsal R, R… Data Brief   <NA>  48           
#>  4 36727245  MED    36727245 PMC1… 10.1… Vasc… Morrissey E… JBI Evid Sy… 5     21           
#>  5 37648680  MED    37648680 <NA>  10.3… [Cli… Liu ZT, Che… Zhonghua Ya… 10    59           
#>  6 37211453  MED    37211453 PMC1… 10.1… Safe… Smith K, He… Vaccine      26    41           
#>  7 37479685  MED    37479685 PMC1… 10.1… SuPA… Wei C, Datt… Nat Commun   1     14           
#>  8 37652823  MED    37652823 <NA>  10.1… Immu… Raiser F, D… Vaccine      <NA>  <NA>         
#>  9 37714559  MED    37714559 <NA>  10.1… New-… Kobayashi N… BMJ Case Rep 9     16           
#> 10 PPR525786 PPR    <NA>     <NA>  10.1… The … Alihsan B, … <NA>         <NA>  <NA>         
#> # ℹ 90 more rows
#> # ℹ 19 more variables: pubYear <chr>, journalIssn <chr>, pageInfo <chr>, pubType <chr>,
#> #   isOpenAccess <chr>, inEPMC <chr>, inPMC <chr>, hasPDF <chr>, hasBook <chr>,
#> #   hasSuppl <chr>, citedByCount <int>, hasReferences <chr>, hasTextMinedTerms <chr>,
#> #   hasDbCrossReferences <chr>, hasLabsLinks <chr>, hasTMAccessionNumbers <chr>,
#> #   firstIndexDate <chr>, firstPublicationDate <chr>, versionNumber <int>

Be aware that Europe PMC expands queries with MeSH synonyms by default. You can turn this behavior off using the synonym = FALSE parameter.

By default, epmc_search() returns 100 records. To adjust the limit, simply use the limit parameter.

See vignette Introducing europepmc, an R interface to Europe PMC RESTful API for a long-form documentation about how to search Europe PMC with this client.

Creating proper review graphs with `epmc_hits_trend()`

There is also a nice function allowing you to easily create review graphs like described in Maëlle Salmon’s blog post:

tt_oa <- europepmc::epmc_hits_trend("Malaria", period = 1995:2019, synonym = FALSE)
tt_oa
#> # A tibble: 25 × 3
#>     year all_hits query_hits
#>    <int>    <dbl>      <dbl>
#>  1  1995   449216       1471
#>  2  1996   458644       1529
#>  3  1997   456804       1834
#>  4  1998   474693       1756
#>  5  1999   493837       1951
#>  6  2000   532142       2078
#>  7  2001   545702       2180
#>  8  2002   561497       2351
#>  9  2003   588612       2596
#> 10  2004   628176       2831
#> # ℹ 15 more rows
# we use ggplot2 for plotting the graph
library(ggplot2)
ggplot(tt_oa, aes(year, query_hits / all_hits)) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of articles on Malaria in Europe PMC")

plot of chunk unnamed-chunk-4

For more info, read the vignette about creating literature review graphs:

https://docs.ropensci.org/europepmc/articles/evergreenreviewgraphs.html

Re-use of europepmc

Check out the tidypmc package

https://github.com/ropensci/tidypmc

The package maintainer, Chris Stubben (@cstubben), has also created an Shiny App that allows you to search and browse Europe PMC:

https://github.com/cstubben/euPMC

Other ways to access Europe PubMed Central

Other APIs

Data dumps: https://europepmc.org/FtpSite
OAI service: https://europepmc.org/OaiService
SOAP web service: https://europepmc.org/SoapWebServices
Grants RESTful (Grist) API: https://europepmc.org/GristAPI

Other R clients

use rOpenSci’s oai to get metadata and full text via Europe PMC’s OAI interface: https://github.com/ropensci/oai
use rOpenSci’s rentrez to interact with NCBI databases such as PubMed: https://github.com/ropensci/rentrez
rOpenSci’s fulltext package gives access to supplementary material of open access life-science publications in Europe PMC: https://github.com/ropensci-archive/fulltext