rcrossref

R interface to various CrossRef APIs

CrossRef documentation

• Crossref API: https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md
• Crossref metadata search API
• CrossRef DOI Content Negotiation
• Text and Data Mining TDM

Installation

Stable version from CRAN

install.packages("rcrossref")

Or development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/rcrossref")

Load rcrossref

library('rcrossref')

Citation search

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

cr_cn(dois = "10.1126/science.169.3946.635", format = "text", style = "apa")
#> [1] "Frank, H. S. (1970). The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance. Science, 169(3946), 635–641. doi:10.1126/science.169.3946.635"

bibtex

cat(cr_cn(dois = "10.1126/science.169.3946.635", format = "bibtex"))
#> @article{Frank_1970,
#> 	doi = {10.1126/science.169.3946.635},
#> 	url = {http://dx.doi.org/10.1126/science.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")
#> Boettiger C (2012). "Regime shifts in ecology and evolution (PhD
#> Dissertation)." doi: 10.6084/m9.figshare.97218 (URL:
#> http://doi.org/10.6084/m9.figshare.97218), <URL:
#> https://doi.org/10.6084/m9.figshare.97218>.

Citation count

Citation count, using OpenURL

cr_citation_count(doi = "10.1371/journal.pone.0042793")
#> [1] 10

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             8          NSF           0             20
#> 
#> $data
#> # A tibble: 8 × 6
#>             id      location
#>          <chr>         <chr>
#> 1    100003187 United States
#> 2    100008367       Denmark
#> 3 501100004190        Norway
#> 4    100000179 United States
#> 5    100006445 United States
#> 6 501100000930     Australia
#> 7    100000001 United States
#> 8 501100001809         China
#> # ... with 4 more variables: name <chr>, alt.names <chr>, uri <chr>,
#> #   tokens <chr>

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)

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        419228           NA           0              1
#> 
#> $data
#> # A tibble: 1 × 24
#>   alternative.id container.title    created  deposited
#>            <chr>           <chr>      <chr>      <chr>
#> 1                                2015-11-11 2015-11-11
#> # ... with 20 more variables: DOI <chr>, funder <list>, indexed <chr>,
#> #   ISBN <chr>, ISSN <chr>, issued <chr>, link <list>, member <chr>,
#> #   prefix <chr>, publisher <chr>, reference.count <chr>, score <chr>,
#> #   source <chr>, subject <chr>, title <chr>, type <chr>, URL <chr>,
#> #   assertion <list>, author <list>, `clinical-trial-number` <list>
#> 
#> $facets
#> NULL

Search journals

cr_journals(issn = c('1803-2427','2326-4225'))
#> # A tibble: 2 × 16
#>   alternative.id container.title created deposited funder indexed  ISBN
#>            <chr>           <chr>   <chr>     <chr> <list>   <chr> <chr>
#> 1                                                  <NULL>              
#> 2                                                  <NULL>              
#> # ... with 9 more variables: ISSN <chr>, issued <chr>, link <list>,
#> #   publisher <chr>, subject <chr>, title <chr>, assertion <list>,
#> #   author <list>, `clinical-trial-number` <list>

Search license information

cr_licenses(query = 'elsevier')
#> $meta
#>   total_results search_terms start_index items_per_page
#> 1            13     elsevier           0             20
#> 
#> $data
#> # A tibble: 13 × 2
#>                                                                            URL
#>                                                                          <chr>
#> 1                            http://creativecommons.org/licenses/by-nc-nd/3.0/
#> 2                            http://creativecommons.org/licenses/by-nc-nd/4.0/
#> 3                               http://creativecommons.org/licenses/by-nc/4.0/
#> 4                                  http://creativecommons.org/licenses/by/3.0/
#> 5                                  http://creativecommons.org/licenses/by/4.0/
#> 6                                   http://doi.wiley.com/10.1002/tdm_license_1
#> 7                            http://onlinelibrary.wiley.com/termsAndConditions
#> 8         http://www.acm.org/publications/policies/copyright_policy#Background
#> 9                         http://www.elsevier.com/open-access/userlicense/1.0/
#> 10                                http://www.elsevier.com/tdm/userlicense/1.0/
#> 11                                                 http://www.springer.com/tdm
#> 12 © 2007 Elsevier Masson SAS. All rights reserved. The patient figure in Figu
#> 13 © 2012, Elsevier Inc., All Rights Reserved. Figure 8, part (B) (images of H
#> # ... with 1 more variables: work.count <int>

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 Nature
#> 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            18      ecology           0              5
#> 
#> $data
#> # A tibble: 5 × 48
#>      id
#>   <int>
#> 1  7052
#> 2  6933
#> 3  7278
#> 4  7745
#> 5  9167
#> # ... with 47 more variables: primary_name <chr>, location <chr>,
#> #   last_status_check_time <date>, backfile.dois <chr>,
#> #   current.dois <chr>, total.dois <chr>, prefixes <chr>,
#> #   coverge.affiliations.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.orcids.current <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.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.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.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.licenses.current <chr>, names <chr>, tokens <chr>
#> 
#> $facets
#> NULL

Get N random DOIs

cr_r() uses the function cr_works() internally.

cr_r()
#>  [1] "10.1039/ct8885300641"                
#>  [2] "10.1063/1.1709474"                   
#>  [3] "10.1111/j.1708-8305.1996.tb00750.x"  
#>  [4] "10.1037//1076-898x.2.3.270"          
#>  [5] "10.4337/9781783471171.00028"         
#>  [6] "10.1007/978-1-349-07777-9_4"         
#>  [7] "10.1111/b.9781405116749.2003.00054.x"
#>  [8] "10.1016/j.crvi.2004.09.010"          
#>  [9] "10.1002/uog.15794"                   
#> [10] "10.14731/kjis.2013.12.11.2.295"

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

cr_r(2)
#> [1] "10.1038/scibx.2008.713"          "10.1007/978-3-642-41714-6_91906"

pmid2doi & doi2pmid

DOIs to PMIDs

UPDATE: as of 2014-12-23 the web API behind these functions is down - we'll update the package once the API is up again

Get full text links to works

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 http://tdmsupport.crossref.org/.

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] "10.1063/1.4905711" "10.1063/1.4908245" "10.1063/1.4908158"
#>  [4] "10.1063/1.4908244" "10.1063/1.4913247" "10.1063/1.4914847"
#>  [7] "10.1063/1.4916217" "10.1063/1.4916677" "10.1063/1.4916696"
#> [10] "10.1063/1.4917283" "10.1063/1.4918284" "10.1063/1.4919707"
#> [13] "10.1063/1.4921711" "10.1063/1.4921771" "10.1063/1.4922319"
#> [16] "10.1063/1.4922934" "10.1063/1.4922006" "10.1063/1.4926610"
#> [19] "10.1063/1.4926838" "10.1063/1.4926914"

Then get URLs to full text content

(links <- cr_ft_links(dois[1]))
#> NULL

Then use those URLs to get full text

cr_ft_text(links, "xml")
#> <?xml version="1.0"?>
#> <article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://jats.nlm.nih.gov/publishing/1.1d1/xsd/JATS-journalpublishing1-mathml3.xsd" dtd-version="1.1d1">
#>   <front>
#>     <journal-meta>
#>       <journal-id journal-id-type="publisher-id">SV</journal-id>
#>       <journal-title-group>
#>         <journal-title>Shock and Vibration</journal-title>
#>       </journal-title-group>
#>       <issn pub-type="epub">1875-9203</issn>
#>       <issn pub-type="ppub">1070-9622</issn>
#>       <publisher>
#>         <publisher-name>Hindawi Publishing Corporation</publisher-name>
#>       </publisher>
#>     </journal-meta>
#> .................... cutoff

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for rcrossref in R doing citation(package = 'rcrossref')
• Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

This package is part of a richer suite called fulltext, along with several other packages, that provides the ability to search for and retrieve full text of open access scholarly articles.