Overview

What is searched?

Europe PMC is a repository of life science literature. Europe PMC ingests all PubMed content and extends its index with other literature and patent sources.

For more background on Europe PMC, see:

https://europepmc.org/About

Levchenko, M., Gou, Y., Graef, F., Hamelers, A., Huang, Z., Ide-Smith, M., … McEntyre, J. (2017). Europe PMC in 2017. Nucleic Acids Research, 46(D1), D1254–D1260. https://doi.org/10.1093/nar/gkx1005

How to search Europe PMC with R?

This client supports the Europe PMC search syntax. If you are unfamiliar with searching Europe PMC, check out the Europe PMC query builder, a very nice tool that helps you to build queries. To make use of Europe PMC queries in R, copy & paste the search string to the search functions of this package.

In the following, some examples demonstrate how to search Europe PMC with R.

Free search

empc_search() is the main function to query Europe PMC. It searches both metadata and fulltexts.

library(europepmc)
europepmc::epmc_search('malaria')
#> # 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 36419237 MED    36419237 PMC98… 10.1… Path… Walker IS, … Virulence    1     14           
#>  2 37158217 MED    37158217 PMC10… 10.1… Mobi… Kollipara A… Glob Health… 1     16           
#>  3 37459385 MED    37459385 PMC10… 10.1… A co… Eisenberg S… Glob Health… 1     16           
#>  4 37310126 MED    37310126 PMC10… 10.1… Clin… Bi D, Huang… Ann Med      1     55           
#>  5 36871259 MED    36871259 PMC99… 10.1… Asse… Jantausch B… Med Educ On… 1     28           
#>  6 37053493 MED    37053493 <NA>   10.1… Opti… Kalula A, M… J Biol Dyn   1     17           
#>  7 37191627 MED    37191627 PMC10… 10.1… Huma… Ellis R, We… Hum Vaccin … 1     19           
#>  8 37490025 MED    37490025 PMC10… 10.1… Mort… Oduor C, Om… Glob Health… 1     16           
#>  9 37165851 MED    37165851 PMC10… 10.1… Tria… Cho Y, Awoo… Glob Health… 1     16           
#> 10 37074313 MED    37074313 PMC99… 10.1… Deng… Asaga Mac P… Ann Med      1     55           
#> # 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>

It is worth noting that Europe PMC expands queries with MeSH synonyms by default, a behavior which can be turned off with the synonym parameter.

europepmc::epmc_search('malaria', synonym = FALSE)
#> # 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 37158217 MED    37158217 PMC10… 10.1… Mobi… Kollipara A… Glob Health… 1     16           
#>  2 36419237 MED    36419237 PMC98… 10.1… Path… Walker IS, … Virulence    1     14           
#>  3 37459385 MED    37459385 PMC10… 10.1… A co… Eisenberg S… Glob Health… 1     16           
#>  4 37053493 MED    37053493 <NA>   10.1… Opti… Kalula A, M… J Biol Dyn   1     17           
#>  5 37310126 MED    37310126 PMC10… 10.1… Clin… Bi D, Huang… Ann Med      1     55           
#>  6 36871259 MED    36871259 PMC99… 10.1… Asse… Jantausch B… Med Educ On… 1     28           
#>  7 37717079 MED    37717079 PMC10… 10.1… Zoon… Fornace KM,… Nat Commun   1     14           
#>  8 37691114 MED    37691114 PMC10… 10.1… Mala… Chen Y, Zha… Malar J      1     22           
#>  9 37700307 MED    37700307 PMC10… 10.1… Asse… Abdul Rahim… Malar J      1     22           
#> 10 37700321 MED    37700321 PMC10… 10.1… Know… Adum P, Agy… Malar J      1     22           
#> # 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>

To get an exact match, use quotes as in the following example:

europepmc::epmc_search('"Human malaria parasites"')
#> # A tibble: 100 × 29
#>    id        source pmid   doi   title authorString journalTitle issue journalVolume pubYear
#>    <chr>     <chr>  <chr>  <chr> <chr> <chr>        <chr>        <chr> <chr>         <chr>  
#>  1 37277533  MED    37277… 10.1… Sexu… Harris CT, … Nat Microbi… 7     8             2023   
#>  2 36777671  MED    36777… 10.3… A no… Das R, Vash… Front Vet S… <NA>  10            2023   
#>  3 37696509  MED    37696… 10.4… A No… Chaianantak… Am J Trop M… <NA>  <NA>          2023   
#>  4 37365785  MED    37365… 10.2… Virt… Yasir M, Pa… Curr Comput… <NA>  <NA>          2023   
#>  5 37454671  MED    37454… 10.1… Simi… Fornace KM,… Lancet Infe… <NA>  <NA>          2023   
#>  6 PPR665403 PPR    <NA>   10.1… Gene… Suárez-Cort… <NA>         <NA>  <NA>          2023   
#>  7 36007706  MED    36007… 10.1… Bulk… Li X, Kumar… Parasitol I… <NA>  91            2022   
#>  8 PPR552791 PPR    <NA>   10.1… A co… Zhang X, Fl… <NA>         <NA>  <NA>          2022   
#>  9 37121862  MED    37121… 10.1… The … Thompson TA… Trends Para… 7     39            2023   
#> 10 36495929  MED    36495… 10.1… A ra… Dong L, Li … Clin Chim A… <NA>  539           2023   
#> # ℹ 90 more rows
#> # ℹ 19 more variables: 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>, pmcid <chr>, versionNumber <int>

Managing search results

By default, 100 records are returned, but the number of results can be expanded or limited with the limit parameter.

europepmc::epmc_search('"Human malaria parasites"', limit = 10)
#> # A tibble: 10 × 28
#>    id        source pmid   doi   title authorString journalTitle issue journalVolume pubYear
#>    <chr>     <chr>  <chr>  <chr> <chr> <chr>        <chr>        <chr> <chr>         <chr>  
#>  1 37277533  MED    37277… 10.1… Sexu… Harris CT, … Nat Microbi… 7     8             2023   
#>  2 36777671  MED    36777… 10.3… A no… Das R, Vash… Front Vet S… <NA>  10            2023   
#>  3 37696509  MED    37696… 10.4… A No… Chaianantak… Am J Trop M… <NA>  <NA>          2023   
#>  4 37365785  MED    37365… 10.2… Virt… Yasir M, Pa… Curr Comput… <NA>  <NA>          2023   
#>  5 37454671  MED    37454… 10.1… Simi… Fornace KM,… Lancet Infe… <NA>  <NA>          2023   
#>  6 PPR665403 PPR    <NA>   10.1… Gene… Suárez-Cort… <NA>         <NA>  <NA>          2023   
#>  7 36007706  MED    36007… 10.1… Bulk… Li X, Kumar… Parasitol I… <NA>  91            2022   
#>  8 PPR552791 PPR    <NA>   10.1… A co… Zhang X, Fl… <NA>         <NA>  <NA>          2022   
#>  9 37121862  MED    37121… 10.1… The … Thompson TA… Trends Para… 7     39            2023   
#> 10 36495929  MED    36495… 10.1… A ra… Dong L, Li … Clin Chim A… <NA>  539           2023   
#> # ℹ 18 more variables: 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>, pmcid <chr>

Results are sorted by relevance. Other options via the sort parameter are

sort = 'cited' by the number of citation, descending from the most cited publication
sort = 'date' by date published starting with the most recent publication

Search by DOIs

Sometimes, you would like to check, if articles are indexed in Europe PMC using DOI names, a widely used identifier for scholarly articles. Use epmc_search_by_doi() for this purpose.

my_dois <- c(
  "10.1159/000479962",
  "10.1002/sctm.17-0081",
  "10.1161/strokeaha.117.018077",
  "10.1007/s12017-017-8447-9"
  )
europepmc::epmc_search_by_doi(doi = my_dois)
#> # A tibble: 4 × 28
#>   id       source pmid     doi   title authorString journalTitle issue journalVolume pubYear
#>   <chr>    <chr>  <chr>    <chr> <chr> <chr>        <chr>        <chr> <chr>         <chr>  
#> 1 28957815 MED    28957815 10.1… Clin… Schnieder M… Eur Neurol   5-6   78            2017   
#> 2 28941317 MED    28941317 10.1… Conc… Doeppner TR… Stem Cells … 11    6             2017   
#> 3 29018132 MED    29018132 10.1… One-… Psychogios … Stroke       11    48            2017   
#> 4 28623611 MED    28623611 10.1… Defe… Carboni E, … Neuromolecu… 2-3   19            2017   
#> # ℹ 18 more variables: 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>, pmcid <chr>

Output options

By default, a non-nested data frame printed as tibble is returned. Other formats are output = "id_list" returning a list of IDs and sources, and output = “‘raw’”” for getting full metadata as list. Please be aware that these lists can become very large.

More advanced options to search Europe PMC

Author search

Use the Europe PMC query syntax to search by author names:

europepmc::epmc_search('AUTH:"Salmon Maelle"')
#> # A tibble: 10 × 28
#>    id       source pmid    doi   title authorString journalTitle issue journalVolume pubYear
#>    <chr>    <chr>  <chr>   <chr> <chr> <chr>        <chr>        <chr> <chr>         <chr>  
#>  1 30378432 MED    303784… 10.1… "Whe… Milà C, Sal… Environ Sci… 22    52            2018   
#>  2 29778830 MED    297788… 10.1… "Wea… Salmon M, M… Environ Int  <NA>  117           2018   
#>  3 29751338 MED    297513… 10.1… "Use… Kumar MK, S… Environ Pol… <NA>  239           2018   
#>  4 29330030 MED    293300… 10.1… "Hea… Mueller N, … Prev Med     <NA>  109           2018   
#>  5 29626773 MED    296267… 10.1… "Dev… Sanchez M, … Sci Total E… <NA>  634           2018   
#>  6 29088243 MED    290882… 10.1… "Tim… Schumacher … PLoS One     10    12            2017   
#>  7 28606699 MED    286066… 10.1… "Int… Tonne C, Sa… Int J Hyg E… 6     220           2017   
#>  8 28708095 MED    287080… 10.3… "Pre… Sanchez M, … Int J Envir… 7     14            2017   
#>  9 27063588 MED    270635… 10.2… "A s… Salmon M, S… Euro Survei… 13    21            2016   
#> 10 26250543 MED    262505… 10.1… "Bay… Salmon M, S… Biom J       6     57            2015   
#> # ℹ 18 more variables: 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>, pmcid <chr>

Europe PMC Advanced Search has a auto-suggest field for author names if you feel unsure how the name you are searching for is indexed in Europe PMC. Using the Boolean OR operator allows searching for more than one spelling variant:

q <- 'AUTH:"PÜHLER Alfred" OR AUTH:"Pühler Alfred Prof. Dr." OR AUTH:"Puhler A"'
europepmc::epmc_search(q, limit = 1000)
#> # A tibble: 600 × 29
#>    id       source pmid     pmcid  doi   title authorString journalTitle issue journalVolume
#>    <chr>    <chr>  <chr>    <chr>  <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 36998097 MED    36998097 PMC10… 10.1… "Abu… Nelkner J, … Environ Mic… 1     18           
#>  2 36748496 MED    36748496 <NA>   10.1… "<i>… Köller N, H… Int J Syst … 12    72           
#>  3 36439843 MED    36439843 PMC96… 10.3… "The… Maus I, Wib… Front Micro… <NA>  13           
#>  4 36305336 MED    36305336 PMC96… 10.2… "Int… Houwaart T,… Euro Survei… 43    27           
#>  5 36073816 MED    36073816 PMC96… 10.1… "Rcg… Castellani … mBio         5     13           
#>  6 35151713 MED    35151713 <NA>   10.1… "Two… Steffens T,… J Biotechnol <NA>  347          
#>  7 34181711 MED    34181711 PMC84… 10.1… "Cha… Walker A, H… Clin Infect… 6     74           
#>  8 34682252 MED    34682252 PMC85… 10.3… "Gen… Wibberg D, … J Fungi (Ba… 10    7            
#>  9 34592166 MED    34592166 PMC84… 10.1… "Ear… Krämer B, K… Immunity     11    54           
#> 10 33589928 MED    33589928 PMC84… 10.1… "Imp… Mayer G, Mü… Brief Bioin… 5     22           
#> # ℹ 590 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>

There is a considerable overlap between common names. The integration of ORCID, a persistent author identifier, allows unambiguous search for personal publications in Europe PMC. For example, here’s how to search for publications written by Bernd Weisshaar (ORCID: https://orcid.org/0000-0002-7635-3473) sorted by the number of times cited in descending order:

europepmc::epmc_search('AUTHORID:"0000-0002-7635-3473"', limit = 200, sort = "cited")
#> # A tibble: 160 × 28
#>    id       source pmid    doi   title authorString journalTitle issue journalVolume pubYear
#>    <chr>    <chr>  <chr>   <chr> <chr> <chr>        <chr>        <chr> <chr>         <chr>  
#>  1 20674465 MED    206744… 10.1… MYB … Dubos C, St… Trends Plan… 10    15            2010   
#>  2 21873998 MED    218739… 10.1… The … Wang X, Wan… Nat Genet    10    43            2011   
#>  3 11597504 MED    115975… 10.1… The … Stracke R, … Curr Opin P… 5     4             2001   
#>  4 11906833 MED    119068… 10.1… bZIP… Jakoby M, W… Trends Plan… 3     7             2002   
#>  5 14756321 MED    147563… 10.1… An A… Rosso MG, L… Plant Mol B… 1-2   53            2003   
#>  6 12679534 MED    126795… 10.1… The … Heim MA, Ja… Mol Biol Ev… 5     20            2003   
#>  7 17419845 MED    174198… 10.1… Diff… Stracke R, … Plant J      4     50            2007   
#>  8 15255866 MED    152558… 10.1… TT2,… Baudry A, H… Plant J      3     39            2004   
#>  9 11080161 MED    110801… 10.1… Tran… Jin H, Comi… EMBO J       22    19            2000   
#> 10 15361138 MED    153611… 10.1… Comp… Zimmermann … Plant J      1     40            2004   
#> # ℹ 150 more rows
#> # ℹ 18 more variables: 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>, pmcid <chr>

Annotations

Europe PMC provides text-mined annotations contained in abstracts and open access full-text articles.

These automatically identified concepts and term can be retrieved at the article-level:

europepmc::epmc_annotations_by_id(c("MED:28585529", "PMC:PMC1664601"))
#> # A tibble: 724 × 13
#>    source ext_id pmcid prefix exact postfix name  uri   id    type  section provider subType
#>    <chr>  <chr>  <chr> <chr>  <chr> <chr>   <chr> <chr> <chr> <chr> <chr>   <chr>    <chr>  
#>  1 MED    28585… PMC5… "tive… Beta… " allo… Beta… http… http… Clin… Title … OntoGene <NA>   
#>  2 MED    28585… PMC5… "nomi… genes ".\nRa… gene  http… http… Sequ… Title … OntoGene <NA>   
#>  3 MED    28585… PMC5… "nomi… genes " is o… gene  http… http… Sequ… Abstra… OntoGene <NA>   
#>  4 MED    28585… PMC5… " One… genes " are … gene  http… http… Sequ… Abstra… OntoGene <NA>   
#>  5 MED    28585… PMC5… " ide… beet  " (Bet… Beta… http… http… Clin… Abstra… OntoGene <NA>   
#>  6 MED    28585… PMC5… "ify … Beta… " ssp.… Beta… http… http… Clin… Abstra… OntoGene <NA>   
#>  7 MED    28585… PMC5… "ulga… gene  " Rz2 … gene  http… http… Sequ… Abstra… OntoGene <NA>   
#>  8 MED    28585… PMC5… "e ge… geno… " sequ… geno… http… http… Sequ… Abstra… OntoGene <NA>   
#>  9 MED    28585… PMC5… "eque… beet  ". Our… Beta… http… http… Clin… Abstra… OntoGene <NA>   
#> 10 MED    28585… PMC5… "disc… genes " rele… gene  http… http… Sequ… Abstra… OntoGene <NA>   
#> # ℹ 714 more rows

To obtain a list of articles where Europe PMC has text-minded annotations, either subset the resulting data.frame

tt <- epmc_search("malaria")
tt[tt$hasTextMinedTerms == "Y" | tt$hasTMAccessionNumbers == "Y",]
#> # A tibble: 96 × 29
#>    id       source pmid     pmcid  doi   title authorString journalTitle issue journalVolume
#>    <chr>    <chr>  <chr>    <chr>  <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 36419237 MED    36419237 PMC98… 10.1… Path… Walker IS, … Virulence    1     14           
#>  2 37158217 MED    37158217 PMC10… 10.1… Mobi… Kollipara A… Glob Health… 1     16           
#>  3 37459385 MED    37459385 PMC10… 10.1… A co… Eisenberg S… Glob Health… 1     16           
#>  4 37310126 MED    37310126 PMC10… 10.1… Clin… Bi D, Huang… Ann Med      1     55           
#>  5 36871259 MED    36871259 PMC99… 10.1… Asse… Jantausch B… Med Educ On… 1     28           
#>  6 37053493 MED    37053493 <NA>   10.1… Opti… Kalula A, M… J Biol Dyn   1     17           
#>  7 37191627 MED    37191627 PMC10… 10.1… Huma… Ellis R, We… Hum Vaccin … 1     19           
#>  8 37490025 MED    37490025 PMC10… 10.1… Mort… Oduor C, Om… Glob Health… 1     16           
#>  9 37165851 MED    37165851 PMC10… 10.1… Tria… Cho Y, Awoo… Glob Health… 1     16           
#> 10 37074313 MED    37074313 PMC99… 10.1… Deng… Asaga Mac P… Ann Med      1     55           
#> # ℹ 86 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>

or expand the query choosing an annotation type or provider from the Europe PMC Advanced Search query builder.

epmc_search('malaria AND (ANNOTATION_TYPE:"Cell") AND (ANNOTATION_PROVIDER:"Europe PMC")')
#> # A tibble: 100 × 28
#>    id       source pmid    doi   title authorString journalTitle issue journalVolume pubYear
#>    <chr>    <chr>  <chr>   <chr> <chr> <chr>        <chr>        <chr> <chr>         <chr>  
#>  1 30925567 MED    309255… 10.1… Cong… Fatima S, S… Pediatr Eme… 12    37            2021   
#>  2 31808816 MED    318088… 10.1… Reti… Villaverde … J Pediatric… 5     9             2020   
#>  3 31782768 MED    317827… 10.1… Incr… Jongo SA, C… Clin Infect… 11    71            2020   
#>  4 30989220 MED    309892… 10.1… Clin… Enane LA, S… J Pediatric… 3     9             2020   
#>  5 31300826 MED    313008… 10.1… Blac… Opoka RO, W… Clin Infect… 11    70            2020   
#>  6 31505001 MED    315050… 10.1… Acut… Oshomah-Bel… J Trop Pedi… 2     66            2020   
#>  7 31687768 MED    316877… 10.1… Eval… Ferdinand D… Trans R Soc… 3     114           2020   
#>  8 31693130 MED    316931… 10.1… Redu… Kingston HW… J Infect Dis 9     221           2020   
#>  9 31843017 MED    318430… 10.1… Arte… Pull L, Lup… Malar J      1     18            2019   
#> 10 31864353 MED    318643… 10.1… Unde… Adhikari SR… Malar J      1     18            2019   
#> # ℹ 90 more rows
#> # ℹ 18 more variables: 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>, pmcid <chr>

Data integrations

Another nice feature of Europe PMC is to search for cross-references between Europe PMC to other databases. For instance, to get publications cited by entries in the Protein Data bank in Europe published 2016:

europepmc::epmc_search('(HAS_PDB:y) AND FIRST_PDATE:2016')
#> # A tibble: 100 × 28
#>    id       source pmid     pmcid  doi   title authorString journalTitle issue journalVolume
#>    <chr>    <chr>  <chr>    <chr>  <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 28039433 MED    28039433 PMC52… 10.1… "Str… Su HP, Rick… Proc Natl A… 3     114          
#>  2 28036383 MED    28036383 PMC52… 10.1… "Str… Kovaľ T, Øs… PLoS One     12    11           
#>  3 27977122 MED    27977122 <NA>   10.1… "Com… De Deurwaer… ACS Chem Ne… 5     8            
#>  4 28144358 MED    28144358 PMC52… 10.3… "Bio… Ulrich V, B… Beilstein J… <NA>  12           
#>  5 28028551 MED    28028551 <NA>   10.1… "Str… Zhou Z, Liu… Appl Microb… 7     101          
#>  6 27958736 MED    27958736 <NA>   10.1… "Gly… Hamark C, B… J Am Chem S… 1     139          
#>  7 27959534 MED    27959534 PMC66… 10.1… "Str… Reed AJ, Vy… J Am Chem S… 1     139          
#>  8 27989121 MED    27989121 PMC58… 10.1… "Sho… Lin J, Pozh… Biochemistry 2     56           
#>  9 27815281 MED    27815281 PMC52… 10.1… "Str… Wakamatsu T… Appl Enviro… 2     83           
#> 10 28083536 MED    28083536 PMC51… 10.3… "Con… Paoletti F,… Front Mol B… <NA>  3            
#> # ℹ 90 more rows
#> # ℹ 18 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>

The following sources are supported

CHEBI a database and ontology of chemical entities of biological interest https://www.ebi.ac.uk/chebi/
CHEMBL a database of bioactive drug-like small molecules https://www.ebi.ac.uk/chembldb/
EMBL now ENA, provides a comprehensive record of the world’s nucleotide sequencing information https://www.ebi.ac.uk/ena/browser/
INTACT provides a freely available, open source database system and analysis tools for molecular interaction data https://www.ebi.ac.uk/intact/
INTERPRO provides functional analysis of proteins by classifying them into families and predicting domains and important sites https://www.ebi.ac.uk/interpro/
OMIM a comprehensive and authoritative compendium of human genes and genetic phenotypes https://www.omim.org/about
PDB European resource for the collection, organisation and dissemination of data on biological macromolecular structures https://www.ebi.ac.uk/pdbe/
UNIPROT comprehensive and freely accessible resource of protein sequence and functional information https://www.uniprot.org/
PRIDE PRIDE Archive - proteomics data repository https://www.ebi.ac.uk/pride/archive/

To retrieve metadata about these external database links, use europepmc_epmc_db().

Citations and reference sections

Europe PMC let us also obtain citation metadata and reference sections. For retrieving citation metadata per article, use

europepmc::epmc_citations("9338777", limit = 500)
#> # A tibble: 241 × 11
#>    id       source citationType  title authorString journalAbbreviation pubYear volume issue
#>    <chr>    <chr>  <chr>         <chr> <chr>        <chr>                 <int> <chr>  <chr>
#>  1 37605152 MED    research sup… "Ana… Flecks M, F… Retrovirology          2023 20     1    
#>  2 36883860 MED    research sup… "Iso… Rodrigues C… J Virol                2023 97     3    
#>  3 36790562 MED    review; jour… "Por… Liu Y, Niu … Funct Integr Genom…    2023 23     1    
#>  4 36417007 MED    research-art… "Hum… Lowe JWE.    Hist Philos Life S…    2022 44     4    
#>  5 35729348 MED    research sup… "Det… Ishihara S,… Sci Rep                2022 12     1    
#>  6 35437972 MED    research-art… "Sca… Chen JQ, Zh… Zool Res               2022 43     3    
#>  7 34834962 MED    im; research… "Por… Denner J.    Viruses                2021 13     11   
#>  8 34578447 MED    im; research… "Hig… Denner J, S… Viruses                2021 13     9    
#>  9 33353186 MED    im; review-a… "Xen… Galow AM, G… Int J Mol Sci          2020 21     24   
#> 10 31565893 MED    research-art… "Reg… Chung HC, N… J Vet Sci              2019 20     5    
#> # ℹ 231 more rows
#> # ℹ 2 more variables: pageInfo <chr>, citedByCount <int>

For reference section from an article:

europepmc::epmc_refs("28632490", limit = 200)
#> # A tibble: 169 × 19
#>    id       source citationType  title authorString journalAbbreviation issue pubYear volume
#>    <chr>    <chr>  <chr>         <chr> <chr>        <chr>               <chr>   <int> <chr> 
#>  1 12002480 MED    JOURNAL ARTI… Tric… Adolfsson-E… Chemosphere         9-10     2002 46    
#>  2 18795164 MED    JOURNAL ARTI… In v… Ahn KC, Zha… Environ Health Per… 9        2008 116   
#>  3 18556606 MED    JOURNAL ARTI… Effe… Aiello AE, … Am J Public Health  8        2008 98    
#>  4 17683018 MED    JOURNAL ARTI… Cons… Aiello AE, … Clin Infect Dis     <NA>     2007 45 Su…
#>  5 15273108 MED    JOURNAL ARTI… Rela… Aiello AE, … Antimicrob Agents … 8        2004 48    
#>  6 18207219 MED    JOURNAL ARTI… The … Allmyr M, H… Sci Total Environ   1        2008 393   
#>  7 17007908 MED    JOURNAL ARTI… Tric… Allmyr M, A… Sci Total Environ   1        2006 372   
#>  8 26948762 MED    JOURNAL ARTI… Pres… Alvarez-Riv… J Chromatogr A      <NA>     2016 1440  
#>  9 23192912 MED    JOURNAL ARTI… Expo… Anderson SE… Toxicol Sci         1        2012 132   
#> 10 25837385 MED    JOURNAL ARTI… Obse… Vladar EK, … Methods Cell Biol   <NA>     2015 127   
#> # ℹ 159 more rows
#> # ℹ 10 more variables: pageInfo <chr>, citedOrder <int>, match <chr>, essn <chr>,
#> #   issn <chr>, publicationTitle <chr>, publisherLoc <chr>, publisherName <chr>,
#> #   externalLink <chr>, doi <chr>

Fulltext access

Europe PMC gives not only access to metadata, but also to full-texts. Adding AND (OPEN_ACCESS:y) to your search query, returns only those articles where Europe PMC has also the fulltext.

Fulltext as xml document can accessed via the PMID or the PubMed Central ID (PMCID):

europepmc::epmc_ftxt("PMC3257301")
#> {xml_document}
#> <article article-type="research-article" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML">
#> [1] <front>\n  <journal-meta>\n    <journal-id journal-id-type="nlm-ta">PLoS Pathog</jour ...
#> [2] <body>\n  <sec id="s1">\n    <title>Introduction</title>\n    <p>Atmospheric carbon d ...
#> [3] <back>\n  <ack>\n    <p>We would like to thank Dr. C. Gourlay and Dr. T. von der Haar ...

Najko Jahn

2023-09-20