Introducing europepmc, an R interface to Europe PMC RESTful API

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 x 29
#>    id    source pmid  doi   title authorString journalTitle journalVolume
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr>        
#>  1 3279… MED    3279… 10.1… Stra… Lu XM, Le R… Methods Mol… 2170         
#>  2 3204… MED    3204… 10.1… Bala… Drewry LL, … Virulence    11           
#>  3 3204… MED    3204… 10.1… Mode… Olaniyi S, … J Biol Dyn   14           
#>  4 3206… MED    3206… 10.1… Pred… Patel H, Du… Virulence    11           
#>  5 3190… MED    3190… 10.1… Sett… Bucşan AN, … Virulence    11           
#>  6 3240… MED    3240… 10.1… B ce… Hahn WO, Pe… Virulence    11           
#>  7 3286… MED    3286… 10.1… Misd… Iriart X, M… Emerg Micro… 9            
#>  8 3246… MED    3246… 10.1… Back… Xing Y, Guo… J Biol Dyn   14           
#>  9 3282… MED    3282… 10.1… Modi… Eleftheriou… Methods Mol… 2198         
#> 10 3271… MED    3271… 10.1… Mamm… Sutherland … Virulence    11           
#> # … with 90 more rows, and 21 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>, pmcid <chr>, issue <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 x 29
#>    id    source pmid  pmcid doi   title authorString journalTitle issue
#>    <chr> <chr>  <chr> <chr> <chr> <chr> <chr>        <chr>        <chr>
#>  1 3204… MED    3204… PMC7… 10.1… Bala… Drewry LL, … Virulence    1    
#>  2 3279… MED    3279… <NA>  10.1… Stra… Lu XM, Le R… Methods Mol… <NA> 
#>  3 3204… MED    3204… <NA>  10.1… Mode… Olaniyi S, … J Biol Dyn   1    
#>  4 3240… MED    3240… <NA>  10.1… B ce… Hahn WO, Pe… Virulence    1    
#>  5 3286… MED    3286… <NA>  10.1… Misd… Iriart X, M… Emerg Micro… 1    
#>  6 3246… MED    3246… <NA>  10.1… Back… Xing Y, Guo… J Biol Dyn   1    
#>  7 3206… MED    3206… PMC7… 10.1… Pred… Patel H, Du… Virulence    1    
#>  8 3190… MED    3190… PMC6… 10.1… Sett… Bucşan AN, … Virulence    1    
#>  9 3294… MED    3294… <NA>  10.1… Dele… Saito M, Br… Lancet Chil… 10   
#> 10 3271… MED    3271… <NA>  10.1… Mamm… Sutherland … Virulence    1    
#> # … with 90 more rows, and 20 more variables: journalVolume <chr>,
#> #   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 x 28
#>    id    source pmid  doi   title authorString journalTitle pubYear journalIssn
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr>   <chr>      
#>  1 3247… MED    3247… 10.1… C-te… Kimata-Arig… J Biochem    2020    "0021-924x…
#>  2 PPR1… PPR    <NA>  10.1… A dr… Cobb DW, Ku… <NA>         2020     <NA>      
#>  3 3298… MED    3298… 10.1… Moni… Kattenberg … Mol Ecol     2020    "0962-1083…
#>  4 PPR2… PPR    <NA>  10.1… A ma… Marcenac P,… <NA>         2020     <NA>      
#>  5 3192… MED    3192… 10.1… Falc… Rosenthal P… Biochim Bio… 2020    "1570-9639…
#>  6 3249… MED    3249… 10.1… Deve… Lantero E, … J Biomed Na… 2020    "1550-7033…
#>  7 PPR9… PPR    <NA>  10.1… Mala… Kwon H, Rey… <NA>         2019     <NA>      
#>  8 PPR9… PPR    <NA>  10.1… Disr… Subudhi AK,… <NA>         2019     <NA>      
#>  9 PPR1… PPR    <NA>  10.2… A ro… Jivapetthai… <NA>         2019     <NA>      
#> 10 PPR6… PPR    <NA>  10.1… Gene… McLean KJ, … <NA>         2018     <NA>      
#> # … with 90 more rows, and 19 more variables: 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>, issue <chr>, journalVolume <chr>,
#> #   pageInfo <chr>, pmcid <chr>

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 x 27
#>    id    source pmid  doi   title authorString journalTitle pubYear journalIssn
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr>   <chr>      
#>  1 3247… MED    3247… 10.1… C-te… Kimata-Arig… J Biochem    2020    "0021-924x…
#>  2 PPR1… PPR    <NA>  10.1… A dr… Cobb DW, Ku… <NA>         2020     <NA>      
#>  3 3298… MED    3298… 10.1… Moni… Kattenberg … Mol Ecol     2020    "0962-1083…
#>  4 PPR2… PPR    <NA>  10.1… A ma… Marcenac P,… <NA>         2020     <NA>      
#>  5 3192… MED    3192… 10.1… Falc… Rosenthal P… Biochim Bio… 2020    "1570-9639…
#>  6 3249… MED    3249… 10.1… Deve… Lantero E, … J Biomed Na… 2020    "1550-7033…
#>  7 PPR9… PPR    <NA>  10.1… Mala… Kwon H, Rey… <NA>         2019     <NA>      
#>  8 PPR9… PPR    <NA>  10.1… Disr… Subudhi AK,… <NA>         2019     <NA>      
#>  9 PPR1… PPR    <NA>  10.2… A ro… Jivapetthai… <NA>         2019     <NA>      
#> 10 PPR6… PPR    <NA>  10.1… Gene… McLean KJ, … <NA>         2018     <NA>      
#> # … with 18 more variables: 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>, issue <chr>, journalVolume <chr>,
#> #   pageInfo <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 x 28
#>   id    source pmid  doi   title authorString journalTitle issue journalVolume
#>   <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
#> 1 2895… MED    2895… 10.1… Clin… Schnieder M… Eur Neurol   5-6   78           
#> 2 2894… MED    2894… 10.1… Conc… Doeppner TR… Stem Cells … 11    6            
#> 3 2901… MED    2901… 10.1… One-… Psychogios … Stroke       11    48           
#> 4 2862… MED    2862… 10.1… Defe… Carboni E, … Neuromolecu… 2-3   19           
#> # … with 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>, 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 x 28
#>    id    source pmid  doi   title authorString journalTitle issue journalVolume
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 3037… MED    3037… 10.1… When… Milà C, Sal… Environ Sci… 22    52           
#>  2 2977… MED    2977… 10.1… Wear… Salmon M, M… Environ Int  <NA>  117          
#>  3 2975… MED    2975… 10.1… Use … Kumar MK, S… Environ Pol… <NA>  239          
#>  4 2933… MED    2933… 10.1… Heal… Mueller N, … Prev Med     <NA>  109          
#>  5 2962… MED    2962… 10.1… Deve… Sanchez M, … Sci Total E… <NA>  634          
#>  6 2908… MED    2908… 10.1… Time… Schumacher … PLoS One     10    12           
#>  7 2860… MED    2860… 10.1… Inte… Tonne C, Sa… Int J Hyg E… 6     220          
#>  8 2870… MED    2870… 10.3… Pred… Sanchez M, … Int J Envir… 7     14           
#>  9 2706… MED    2706… 10.2… A sy… Salmon M, S… Euro Survei… 13    21           
#> 10 2625… MED    2625… 10.1… Baye… Salmon M, S… Biom J       6     57           
#> # … with 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>, 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: 578 x 28
#>    id    source pmid  doi   title authorString journalTitle issue journalVolume
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 3297… MED    3297… 10.1… pSET… Schaffert L… Microbiol R… 39    9            
#>  2 3281… MED    3281… 10.1… Seve… Schulte-Sch… Cell         6     182          
#>  3 PPR1… PPR    <NA>  10.2… The … Droste J, O… <NA>         <NA>  <NA>         
#>  4 3234… MED    3234… 10.1… Abse… Schaffert L… Appl Microb… 12    104          
#>  5 3186… MED    3186… 10.3… Geno… Hassa J, Wi… Microorgani… 1     8            
#>  6 3173… MED    3173… 10.3… Esse… Schaffert L… Front Micro… <NA>  10           
#>  7 3140… MED    3140… 10.3… Gene… Nelkner J, … Genes (Base… 8     10           
#>  8 3125… MED    3125… 10.1… Eval… Schaffert L… Microb Cell… 1     18           
#>  9 2909… MED    2909… 10.1… A ge… Mayer G, Qu… Brief Bioin… 4     20           
#> 10 3135… MED    3135… 10.1… de.N… Belmann P, … F1000Res     <NA>  8            
#> # … with 568 more rows, and 19 more variables: pubYear <chr>,
#> #   journalIssn <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>, pageInfo <chr>

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: 143 x 28
#>    id    source pmid  doi   title authorString journalTitle issue journalVolume
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr> <chr>        
#>  1 2187… MED    2187… 10.1… The … Wang X, Wan… Nat Genet    10    43           
#>  2 2067… MED    2067… 10.1… MYB … Dubos C, St… Trends Plan… 10    15           
#>  3 1159… MED    1159… 10.1… The … Stracke R, … Curr Opin P… 5     4            
#>  4 1190… MED    1190… 10.1… bZIP… Jakoby M, W… Trends Plan… 3     7            
#>  5 1475… MED    1475… 10.1… An A… Rosso MG, L… Plant Mol B… 1-2   53           
#>  6 1267… MED    1267… 10.1… The … Heim MA, Ja… Mol Biol Ev… 5     20           
#>  7 1108… MED    1108… 10.1… Tran… Jin H, Comi… EMBO J       22    19           
#>  8 1536… MED    1536… 10.1… Comp… Zimmermann … Plant J      1     40           
#>  9 1525… MED    1525… 10.1… TT2,… Baudry A, H… Plant J      3     39           
#> 10 1741… MED    1741… 10.1… Diff… Stracke R, … Plant J      4     50           
#> # … with 133 more rows, and 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>, 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: 774 x 13
#>    source ext_id pmcid prefix exact postfix name  uri   id    type  section
#>    <chr>  <chr>  <chr> <chr>  <chr> <chr>   <chr> <chr> <chr> <chr> <chr>  
#>  1 MED    28585… PMC5… "tive… Beta… " allo… Beta… http… http… Orga… Title …
#>  2 MED    28585… PMC5… "at, … suga… " (Bet… suga… http… http… Orga… Abstra…
#>  3 MED    28585… PMC5… "d a … beet  ". "    beet  http… http… Orga… Abstra…
#>  4 MED    28585… PMC5… "lati… beets " (B. … beets http… http… Orga… Abstra…
#>  5 MED    28585… PMC5… "of <… B. v… " ssp.… B. v… http… http… Orga… Abstra…
#>  6 MED    28585… PMC5… " bee… ssp   ". mar… ssp   http… http… Gene… Abstra…
#>  7 MED    28585… PMC5… "ify … Beta… " ssp.… Beta… http… http… Orga… Abstra…
#>  8 MED    28585… PMC5… "beet… ssp   ". vul… ssp   http… http… Gene… Abstra…
#>  9 MED    28585… PMC5… "ed v… MBS   "). "   MBS   http… http… Gene… Abstra…
#> 10 MED    28585… PMC5… "2 wa… MBS   " and … MBS   http… http… Gene… Abstra…
#> # … with 764 more rows, and 2 more variables: provider <chr>, subType <chr>

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: 71 x 29
#>    id    source pmid  doi   title authorString journalTitle journalVolume
#>    <chr> <chr>  <chr> <chr> <chr> <chr>        <chr>        <chr>        
#>  1 3279… MED    3279… 10.1… Stra… Lu XM, Le R… Methods Mol… 2170         
#>  2 3204… MED    3204… 10.1… Bala… Drewry LL, … Virulence    11           
#>  3 3204… MED    3204… 10.1… Mode… Olaniyi S, … J Biol Dyn   14           
#>  4 3206… MED    3206… 10.1… Pred… Patel H, Du… Virulence    11           
#>  5 3190… MED    3190… 10.1… Sett… Bucşan AN, … Virulence    11           
#>  6 3240… MED    3240… 10.1… B ce… Hahn WO, Pe… Virulence    11           
#>  7 3286… MED    3286… 10.1… Misd… Iriart X, M… Emerg Micro… 9            
#>  8 3246… MED    3246… 10.1… Back… Xing Y, Guo… J Biol Dyn   14           
#>  9 3282… MED    3282… 10.1… Modi… Eleftheriou… Methods Mol… 2198         
#> 10 3294… MED    3294… 10.1… Dele… Saito M, Br… Lancet Chil… 4            
#> # … with 61 more rows, and 21 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>, pmcid <chr>, issue <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 x 28
#>    id    source pmid  pmcid doi   title authorString journalTitle issue
#>    <chr> <chr>  <chr> <chr> <chr> <chr> <chr>        <chr>        <chr>
#>  1 3098… MED    3098… PMC7… 10.1… Clin… Enane LA, S… J Pediatric… 3    
#>  2 3130… MED    3130… PMC7… 10.1… Blac… Opoka RO, W… Clin Infect… 11   
#>  3 3215… MED    3215… PMC7… 10.1… In V… Yao X, Ye F… Clin Infect… 15   
#>  4 3169… MED    3169… PMC7… 10.1… Redu… Kingston HW… J Infect Dis 9    
#>  5 3150… MED    3150… <NA>  10.1… Acut… Oshomah-Bel… J Trop Pedi… 2    
#>  6 3168… MED    3168… <NA>  10.1… Eval… Ferdinand D… Trans R Soc… 3    
#>  7 3167… MED    3167… <NA>  10.1… A Sy… Thiengsusuk… Eur J Drug … 2    
#>  8 3153… MED    3153… <NA>  10.1… Asso… Peitzmeier … AIDS Behav   3    
#>  9 3104… MED    3104… PMC7… 10.1… Elev… Datta D, Co… Clin Infect… 6    
#> 10 3085… MED    3085… <NA>  10.1… An E… Woodford J,… J Infect Dis 6    
#> # … with 90 more rows, and 19 more variables: journalVolume <chr>,
#> #   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>

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 x 28
#>    id    source pmid  pmcid doi   title authorString journalTitle issue
#>    <chr> <chr>  <chr> <chr> <chr> <chr> <chr>        <chr>        <chr>
#>  1 2798… MED    2798… PMC5… 10.1… Shor… Lin J, Pozh… Biochemistry 2    
#>  2 2781… MED    2781… PMC5… 10.1… Stru… Wakamatsu T… Appl Enviro… 2    
#>  3 2803… MED    2803… PMC5… 10.1… Stru… Waz S, Naka… J Biol Chem  7    
#>  4 2803… MED    2803… PMC5… 10.1… Stru… Christensen… PLoS One     12   
#>  5 2806… MED    2806… PMC5… 10.1… Stru… Gai Z, Wang… Cell Discov  <NA> 
#>  6 2802… MED    2802… PMC5… 10.1… Crys… Kuk AC, Mas… Nat Struct … 2    
#>  7 2801… MED    2801… PMC5… 10.1… Stru… Levdikov VM… J Biol Chem  7    
#>  8 2800… MED    2800… PMC5… 10.1… Stru… Zhao H, Wei… Sci Rep      <NA> 
#>  9 2800… MED    2800… PMC6… 10.1… Disc… Cheeseman M… J Med Chem   1    
#> 10 2786… MED    2786… <NA>  10.1… Stru… Bhatt A, Ma… Chembiochem  2    
#> # … with 90 more rows, and 19 more variables: journalVolume <chr>,
#> #   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 http://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 http://www.ebi.ac.uk/ena/
INTACT provides a freely available, open source database system and analysis tools for molecular interaction data http://www.ebi.ac.uk/intact/
INTERPRO provides functional analysis of proteins by classifying them into families and predicting domains and important sites http://www.ebi.ac.uk/interpro/
OMIM a comprehensive and authoritative compendium of human genes and genetic phenotypes http://www.ncbi.nlm.nih.gov/omim
PDB European resource for the collection, organisation and dissemination of data on biological macromolecular structures http://www.ebi.ac.uk/pdbe/
UNIPROT comprehensive and freely accessible resource of protein sequence and functional information http://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: 233 x 11
#>    id    source citationType title authorString journalAbbrevia… pubYear volume
#>    <chr> <chr>  <chr>        <chr> <chr>        <chr>              <int> <chr> 
#>  1 3156… MED    research-ar… Regu… Chung HC, N… J Vet Sci           2019 20    
#>  2 3023… MED    research su… Bioe… Legallais C… Adv Healthc Mat…    2018 7     
#>  3 3026… MED    research su… Porc… Fiebig U, F… Xenotransplanta…    2018 25    
#>  4 2975… MED    historical … Infe… Weiss RA.    Xenotransplanta…    2018 25    
#>  5 2964… MED    research su… Trac… Kawasaki J,… Viruses             2018 10    
#>  6 2876… MED    research su… Pres… Kawasaki J,… J Virol             2017 91    
#>  7 2843… MED    research su… Thre… Colon-Moran… Virology            2017 507   
#>  8 2805… MED    research su… Anti… Inoue Y, Yo… Ann Biomed Eng      2017 45    
#>  9 2783… MED    research-ar… Tran… Kim N, Choi… PLoS One            2016 11    
#> 10 2746… MED    research su… Exis… Kuse K, Ito… J Virol             2016 90    
#> # … with 223 more rows, and 3 more variables: issue <chr>, pageInfo <chr>,
#> #   citedByCount <int>

For reference section from an article:

europepmc::epmc_refs("28632490", limit = 200)
#> # A tibble: 169 x 19
#>    id    source citationType title authorString journalAbbrevia… issue pubYear
#>    <chr> <chr>  <chr>        <chr> <chr>        <chr>            <chr>   <int>
#>  1 1200… MED    JOURNAL ART… Tric… Adolfsson-E… Chemosphere      9-10     2002
#>  2 1879… MED    JOURNAL ART… In v… Ahn KC, Zha… Environ. Health… 9        2008
#>  3 1855… MED    JOURNAL ART… Effe… Aiello AE, … Am J Public Hea… 8        2008
#>  4 1768… MED    JOURNAL ART… Cons… Aiello AE, … Clin. Infect. D… <NA>     2007
#>  5 1527… MED    JOURNAL ART… Rela… Aiello AE, … Antimicrob. Age… 8        2004
#>  6 1820… MED    JOURNAL ART… The … Allmyr M, H… Sci. Total Envi… 1        2008
#>  7 1700… MED    JOURNAL ART… Tric… Allmyr M, A… Sci. Total Envi… 1        2006
#>  8 2694… MED    JOURNAL ART… Pres… Alvarez-Riv… J Chromatogr A   <NA>     2016
#>  9 2319… MED    JOURNAL ART… Expo… Anderson SE… Toxicol. Sci.    1        2012
#> 10 2583… MED    JOURNAL ART… Obse… Vladar EK, … Methods Cell Bi… <NA>     2015
#> # … with 159 more rows, and 11 more variables: volume <chr>, 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  ...
#> [2] <body>\n  <sec id="s1">\n    <title>Introduction</title>\n    <p>Atmosphe ...
#> [3] <back>\n  <ack>\n    <p>We would like to thank Dr. C. Gourlay and Dr. T.  ...

Najko Jahn

2020-10-09