rcrossref introduction

Scott Chamberlain

2020-10-02

Installation

Install stable version from CRAN

install.packages("rcrossref")

Or development version from GitHub

remotes::install_github("ropensci/rcrossref")

library("rcrossref")

Citation search

CrossRef’s DOI Content Negotiation service, where you can citations back in various formats, including apa

cr_cn(dois = "10.1371/journal.pone.0112608", format = "text", style = "apa")
#> [1] "Wang, Q., & Taylor, J. E. (2014). Quantifying Human Mobility Perturbation and Resilience in Hurricane Sandy. PLoS ONE, 9(11), e112608. doi:10.1371/journal.pone.0112608"

There are a lot more styles. We include a dataset as a character vector within the package, accessible via the get_styles() function, e.g.,

get_styles()[1:5]
#> [1] "academy-of-management-review"        
#> [2] "accident-analysis-and-prevention"    
#> [3] "aci-materials-journal"               
#> [4] "acm-sig-proceedings-long-author-list"
#> [5] "acm-sig-proceedings"

bibtex

cat(cr_cn(dois = "10.1126/science.169.3946.635", format = "bibtex"))
#> @article{Frank_1970,
#>  doi = {10.1126/science.169.3946.635},
#>  url = {https://doi.org/10.1126%2Fscience.169.3946.635},
#>  year = 1970,
#>  month = {aug},
#>  publisher = {American Association for the Advancement of Science ({AAAS})},
#>  volume = {169},
#>  number = {3946},
#>  pages = {635--641},
#>  author = {H. S. Frank},
#>  title = {The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance},
#>  journal = {Science}
#> }

bibentry

cr_cn(dois = "10.6084/m9.figshare.97218", format = "bibentry")
#> $doi
#> [1] "10.6084/M9.FIGSHARE.97218"
#> 
#> $url
#> [1] "https://figshare.com/articles/thesis/Regime_shifts_in_ecology_and_evolution_(PhD_Dissertation)/97218"
#> 
#> $author
#> [1] "Boettiger, Carl"
#> 
#> $keywords
#> [1] "Evolutionary Biology, FOS: Biological sciences, FOS: Biological sciences, Ecology"
#> 
#> $title
#> [1] "Regime shifts in ecology and evolution (PhD Dissertation)"
#> 
#> $publisher
#> [1] "figshare"
#> 
#> $year
#> [1] "2012"
#> 
#> $copyright
#> [1] "Creative Commons Attribution 4.0 International"
#> 
#> $key
#> [1] "https://doi.org/10.6084/m9.figshare.97218"
#> 
#> $entry
#> [1] "article"

Citation count

Citation count, using OpenURL

cr_citation_count(doi="10.1371/journal.pone.0042793")
#>                            doi count
#> 1 10.1371/journal.pone.0042793    40

Search Crossref metadata API

The following functions all use the CrossRef API.

Look up funder information

cr_funders(query="NSF")
#> $meta
#>   total_results search_terms start_index items_per_page
#> 1            22          NSF           0             20
#> 
#> $data
#> # A tibble: 20 x 6
#>    id     name            alt.names          uri        tokens          location
#>    <chr>  <chr>           <chr>              <chr>      <chr>           <chr>   
#>  1 50110… National Strok… NSF                http://dx… national, stro… <NA>    
#>  2 50110… National Scien… NSF, National Sci… http://dx… national, scie… <NA>    
#>  3 10000… National Sleep… NSF                http://dx… national, slee… United …
#>  4 50110… Norsk Sykeplei… NSF, Norwegian Nu… http://dx… norsk, sykeple… <NA>    
#>  5 10000… National Scien… USA NSF, NSF, US … http://dx… national, scie… United …
#>  6 10000… Center for Hie… CHM, NSF, Univers… http://dx… center, for, h… United …
#>  7 10001… Arkansas NSF E… Arkansas EPSCoR P… http://dx… arkansas, nsf,… United …
#>  8 10001… Kansas NSF EPS… KNE, NSF EPSCoR    http://dx… kansas, nsf, e… United …
#>  9 50110… Natural Scienc… Anhui Provincial … http://dx… natural, scien… China   
#> 10 10000… Statens Naturv… Danish National S… http://dx… statens, natur… <NA>    
#> 11 10000… Office of the … NSF Office of the… http://dx… office, of, th… United …
#> 12 50110… National Natur… Natural Science F… http://dx… national, natu… China   
#> 13 10001… Nick Simons Fo… NSF, The Nick Sim… http://dx… nick, simons, … United …
#> 14 10001… BioXFEL Scienc… National Science … http://dx… bioxfel, scien… United …
#> 15 10000… Division of In… IOS, NSF Division… http://dx… division, of, … United …
#> 16 50110… NSFC-Henan Joi… NSFC-Henan Provin… http://dx… nsfc, henan, j… China   
#> 17 50110… National Natur… NSFC-Guangdong Jo… http://dx… national, natu… China   
#> 18 50110… Data Center of… Data Center of Ma… http://dx… data, center, … China   
#> 19 50110… National Natur… NSFC-Yunnan Joint… http://dx… national, natu… China   
#> 20 50110… National Natur… NSFC-Shandong Joi… http://dx… national, natu… China   
#> 
#> $facets
#> NULL

Check the DOI minting agency

cr_agency(dois = '10.13039/100000001')
#> $DOI
#> [1] "10.13039/100000001"
#> 
#> $agency
#> $agency$id
#> [1] "crossref"
#> 
#> $agency$label
#> [1] "Crossref"

Search works (i.e., articles, books, etc.)

cr_works(filter=c(has_orcid=TRUE, from_pub_date='2004-04-04'), limit=1)
#> $meta
#>   total_results search_terms start_index items_per_page
#> 1       4738988           NA           0              1
#> 
#> $data
#> # A tibble: 1 x 34
#>   container.title created deposited published.online doi   indexed issn  issue
#>   <chr>           <chr>   <chr>     <chr>            <chr> <chr>   <chr> <chr>
#> 1 Chemical Commu… 2018-1… 2019-11-… 2019             10.1… 2020-0… 1359… 6    
#> # … with 26 more variables: issued <chr>, member <chr>, page <chr>,
#> #   prefix <chr>, publisher <chr>, score <chr>, source <chr>,
#> #   reference.count <chr>, references.count <chr>,
#> #   is.referenced.by.count <chr>, subject <chr>, title <chr>, type <chr>,
#> #   update.policy <chr>, url <chr>, volume <chr>, abstract <chr>,
#> #   language <chr>, short.container.title <chr>, assertion <list>,
#> #   author <list>, funder <list>, link <list>, content_domain <list>,
#> #   license <list>, reference <list>
#> 
#> $facets
#> NULL

Search journals

cr_journals(issn=c('1803-2427','2326-4225'))
#> $data
#> # A tibble: 2 x 53
#>   title publisher issn  last_status_che… deposits_abstra… deposits_orcids…
#>   <chr> <chr>     <chr> <date>           <lgl>            <lgl>           
#> 1 Jour… "De Gruy… 1805… 2020-09-30       TRUE             FALSE           
#> 2 Jour… "America… 2326… 2020-09-29       FALSE            FALSE           
#> # … with 47 more variables: deposits <lgl>,
#> #   deposits_affiliations_backfile <lgl>,
#> #   deposits_update_policies_backfile <lgl>,
#> #   deposits_similarity_checking_backfile <lgl>,
#> #   deposits_award_numbers_current <lgl>,
#> #   deposits_resource_links_current <lgl>, deposits_articles <lgl>,
#> #   deposits_affiliations_current <lgl>, deposits_funders_current <lgl>,
#> #   deposits_references_backfile <lgl>, deposits_abstracts_backfile <lgl>,
#> #   deposits_licenses_backfile <lgl>, deposits_award_numbers_backfile <lgl>,
#> #   deposits_open_references_backfile <lgl>,
#> #   deposits_open_references_current <lgl>, deposits_references_current <lgl>,
#> #   deposits_resource_links_backfile <lgl>, deposits_orcids_backfile <lgl>,
#> #   deposits_funders_backfile <lgl>, deposits_update_policies_current <lgl>,
#> #   deposits_similarity_checking_current <lgl>,
#> #   deposits_licenses_current <lgl>, affiliations_current <dbl>,
#> #   similarity_checking_current <dbl>, funders_backfile <dbl>,
#> #   licenses_backfile <dbl>, funders_current <dbl>,
#> #   affiliations_backfile <dbl>, resource_links_backfile <dbl>,
#> #   orcids_backfile <dbl>, update_policies_current <dbl>,
#> #   open_references_backfile <dbl>, orcids_current <dbl>,
#> #   similarity_checking_backfile <dbl>, references_backfile <dbl>,
#> #   award_numbers_backfile <dbl>, update_policies_backfile <dbl>,
#> #   licenses_current <dbl>, award_numbers_current <dbl>,
#> #   abstracts_backfile <dbl>, resource_links_current <dbl>,
#> #   abstracts_current <dbl>, open_references_current <dbl>,
#> #   references_current <dbl>, total_dois <int>, current_dois <int>,
#> #   backfile_dois <int>
#> 
#> $facets
#> NULL

Search license information

cr_licenses(query = 'elsevier')
#> $meta
#>   total_results search_terms start_index items_per_page
#> 1            39     elsevier           0             20
#> 
#> $data
#> # A tibble: 39 x 2
#>    URL                                                      work.count
#>    <chr>                                                         <int>
#>  1 http://aspb.org/publications/aspb-journals/open-articles          1
#>  2 http://creativecommons.org/licenses/by-nc-nd/3.0/                11
#>  3 http://creativecommons.org/licenses/by-nc-nd/4.0/                16
#>  4 http://creativecommons.org/licenses/by-nc/4.0/                    4
#>  5 http://creativecommons.org/licenses/by/2.0                        2
#>  6 http://creativecommons.org/licenses/by/3.0/                       1
#>  7 http://creativecommons.org/licenses/by/3.0/igo/                   1
#>  8 http://creativecommons.org/licenses/by/4.0                        9
#>  9 http://creativecommons.org/licenses/by/4.0/                      16
#> 10 http://doi.wiley.com/10.1002/tdm_license_1                      136
#> # … with 29 more rows

Search based on DOI prefixes

cr_prefixes(prefixes=c('10.1016','10.1371','10.1023','10.4176','10.1093'))
#> $meta
#> NULL
#> 
#> $data
#>                               member                                    name
#> 1   http://id.crossref.org/member/78                             Elsevier BV
#> 2  http://id.crossref.org/member/340        Public Library of Science (PLoS)
#> 3  http://id.crossref.org/member/297 Springer Science and Business Media LLC
#> 4 http://id.crossref.org/member/1989                    Co-Action Publishing
#> 5  http://id.crossref.org/member/286           Oxford University Press (OUP)
#>                                  prefix
#> 1 http://id.crossref.org/prefix/10.1016
#> 2 http://id.crossref.org/prefix/10.1371
#> 3 http://id.crossref.org/prefix/10.1023
#> 4 http://id.crossref.org/prefix/10.4176
#> 5 http://id.crossref.org/prefix/10.1093
#> 
#> $facets
#> list()

Search CrossRef members

cr_members(query='ecology', limit = 5)
#> $meta
#>   total_results search_terms start_index items_per_page
#> 1            23      ecology           0              5
#> 
#> $data
#> # A tibble: 5 x 56
#>      id primary_name location last_status_che… total.dois current.dois
#>   <int> <chr>        <chr>    <date>           <chr>      <chr>       
#> 1  1950 Journal of … Suite 8… 2020-10-02       0          0           
#> 2  2899 Association… P.O. Bo… 2020-10-02       0          0           
#> 3  4302 Immediate S… Dept. o… 2020-10-02       6          0           
#> 4  7052 Chinese Jou… Flat C … 2020-10-02       1372       251         
#> 5  2467 Ideas in Ec… Prins W… 2020-10-02       0          0           
#> # … with 50 more variables: backfile.dois <chr>, prefixes <chr>,
#> #   coverge.affiliations.current <chr>,
#> #   coverge.similarity.checking.current <chr>, coverge.funders.backfile <chr>,
#> #   coverge.licenses.backfile <chr>, coverge.funders.current <chr>,
#> #   coverge.affiliations.backfile <chr>, coverge.resource.links.backfile <chr>,
#> #   coverge.orcids.backfile <chr>, coverge.update.policies.current <chr>,
#> #   coverge.open.references.backfile <chr>, coverge.orcids.current <chr>,
#> #   coverge.similarity.checking.backfile <chr>,
#> #   coverge.references.backfile <chr>, coverge.award.numbers.backfile <chr>,
#> #   coverge.update.policies.backfile <chr>, coverge.licenses.current <chr>,
#> #   coverge.award.numbers.current <chr>, coverge.abstracts.backfile <chr>,
#> #   coverge.resource.links.current <chr>, coverge.abstracts.current <chr>,
#> #   coverge.open.references.current <chr>, coverge.references.current <chr>,
#> #   flags.deposits.abstracts.current <chr>,
#> #   flags.deposits.orcids.current <chr>, flags.deposits <chr>,
#> #   flags.deposits.affiliations.backfile <chr>,
#> #   flags.deposits.update.policies.backfile <chr>,
#> #   flags.deposits.similarity.checking.backfile <chr>,
#> #   flags.deposits.award.numbers.current <chr>,
#> #   flags.deposits.resource.links.current <chr>, flags.deposits.articles <chr>,
#> #   flags.deposits.affiliations.current <chr>,
#> #   flags.deposits.funders.current <chr>,
#> #   flags.deposits.references.backfile <chr>,
#> #   flags.deposits.abstracts.backfile <chr>,
#> #   flags.deposits.licenses.backfile <chr>,
#> #   flags.deposits.award.numbers.backfile <chr>,
#> #   flags.deposits.open.references.backfile <chr>,
#> #   flags.deposits.open.references.current <chr>,
#> #   flags.deposits.references.current <chr>,
#> #   flags.deposits.resource.links.backfile <chr>,
#> #   flags.deposits.orcids.backfile <chr>,
#> #   flags.deposits.funders.backfile <chr>,
#> #   flags.deposits.update.policies.current <chr>,
#> #   flags.deposits.similarity.checking.current <chr>,
#> #   flags.deposits.licenses.current <chr>, names <chr>, tokens <chr>
#> 
#> $facets
#> NULL

Get N random DOIs

cr_r() uses the function cr_works() internally.

cr_r()
#>  [1] "10.1093/oseo/instance.00086433"    "10.1093/jaoac/49.5.915"           
#>  [3] "10.14814/phy2.13993"               "10.2210/pdb5rnw/pdb"              
#>  [5] "10.1002/ajp.1350150207"            "10.1111/j.1532-950x.2012.01075.x" 
#>  [7] "10.1021/ma00060a006"               "10.1371/journal.pone.0045474.s001"
#>  [9] "10.1086/447083"                    "10.17352/jbm.000021"

You can pass in the number of DOIs you want back (default is 10)

cr_r(2)
#> [1] "10.1525/ncl.1983.38.2.99p0363h" "10.1177/1087057109350114"

Get full text

Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at https://support.crossref.org/hc/en-us/articles/215750183-Crossref-Text-and-Data-Mining-Services

Get some DOIs for articles that provide full text, and that have CC-BY 3.0 licenses (i.e., more likely to actually be open)

out <-
  cr_works(filter = list(has_full_text = TRUE,
    license_url = "http://creativecommons.org/licenses/by/3.0/"))
(dois <- out$data$doi)
#>  [1] "10.1016/s0370-2693(01)01461-7" "10.1016/s0370-2693(01)01505-2"
#>  [3] "10.1016/s0370-2693(01)01497-6" "10.1016/s0370-2693(01)01503-9"
#>  [5] "10.1016/s0370-2693(01)01486-1" "10.1016/s0370-2693(02)01156-5"
#>  [7] "10.1016/s0370-2693(02)01181-4" "10.1016/s0370-2693(01)01471-x"
#>  [9] "10.1016/s0370-2693(01)01467-8" "10.1016/s0370-2693(02)01166-8"
#> [11] "10.1016/s0370-2693(02)01174-7" "10.1016/s0370-2693(02)01179-6"
#> [13] "10.1016/s0370-2693(01)01473-3" "10.1016/s0370-2693(01)01518-0"
#> [15] "10.1016/s0370-2693(01)01512-x" "10.1016/s0370-2693(01)01500-3"
#> [17] "10.1016/s0370-2693(01)01487-3" "10.1016/s0370-2693(01)01431-9"
#> [19] "10.1016/s0370-2693(01)01469-1" "10.1016/s0370-2693(01)01450-2"

From the output of cr_works we can get full text links if we know where to look:

do.call("rbind", out$data$link)
#> # A tibble: 40 x 4
#>    URL                            content.type content.version intended.applica…
#>    <chr>                          <chr>        <chr>           <chr>            
#>  1 https://api.elsevier.com/cont… text/xml     vor             text-mining      
#>  2 https://api.elsevier.com/cont… text/plain   vor             text-mining      
#>  3 https://api.elsevier.com/cont… text/xml     vor             text-mining      
#>  4 https://api.elsevier.com/cont… text/plain   vor             text-mining      
#>  5 https://api.elsevier.com/cont… text/xml     vor             text-mining      
#>  6 https://api.elsevier.com/cont… text/plain   vor             text-mining      
#>  7 https://api.elsevier.com/cont… text/xml     vor             text-mining      
#>  8 https://api.elsevier.com/cont… text/plain   vor             text-mining      
#>  9 https://api.elsevier.com/cont… text/xml     vor             text-mining      
#> 10 https://api.elsevier.com/cont… text/plain   vor             text-mining      
#> # … with 30 more rows

From there, you can grab your full text, but because most links require authentication, enter another package: crminer.

You’ll need package crminer for the rest of the work.

Onc we have DOIs, get URLs to full text content

if (!requireNamespace("crminer")) {
  install.packages("crminer")
}

library(crminer)
(links <- crm_links("10.1155/2014/128505"))
#> $pdf
#> <url> http://downloads.hindawi.com/archive/2014/128505.pdf
#> 
#> $xml
#> <url> http://downloads.hindawi.com/archive/2014/128505.xml
#> 
#> $unspecified
#> <url> http://downloads.hindawi.com/archive/2014/128505.pdf

Then use those URLs to get full text

crm_pdf(links)
#> <document>/Users/sckott/Library/Caches/R/crminer/128505.pdf
#>   Pages: 1
#>   No. characters: 1565
#>   Created: 2014-09-15

See also fulltext (https://github.com/ropensci/fulltext) for getting scholarly text for text mining.