- Crossref API: https://github.com/CrossRef/rest-api-doc#readme
- Crossref's API issue tracker: https://gitlab.com/crossref/issues
- Crossref metadata search API: https://www.crossref.org/labs/crossref-metadata-search/
- Crossref DOI Content Negotiation: https://citation.crosscite.org/docs.html
- Crossref Text and Data Mining (TDM) Services: https://tdmsupport.crossref.org/
Stable version from CRAN
install.packages("rcrossref")Or development version from GitHub
remotes::install_github("ropensci/rcrossref")Load rcrossref
library('rcrossref')If you are intending to access Crossref regularly you will want to send your email address with your queries. This has the advantage that queries are placed in the polite pool of servers. Including your email address is good practice as described in the Crossref documentation under Good manners (https://github.com/CrossRef/rest-api-doc#good-manners--more-reliable-service). The second advantage is that Crossref can contact you if there is a problem with a query.
Details on how to register your email in a call can be found at ?rcrossref-package. To pass your email address to Crossref, simply store it as an environment variable in .Renviron like this:
Open file: file.edit("~/.Renviron")
Add email address to be shared with Crossref crossref_email= "[email protected]"
Save the file and restart your R session
To stop sharing your email when using rcrossref simply delete it from your .Renviron file.
Use CrossRef's DOI Content Negotiation (https://citation.crosscite.org/docs.html) service, where you can get 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 = {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")
#> list()Citation count, using OpenURL
cr_citation_count(doi = "10.1371/journal.pone.0042793")
#> doi count
#> 1 10.1371/journal.pone.0042793 38The following functions all use the CrossRef API https://github.com/CrossRef/rest-api-doc#readme
cr_funders(query = "NSF")
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 17 NSF 0 20
#>
#> $data
#> # A tibble: 17 x 6
#> id name alt.names uri tokens location
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 50110… National Scien… NSF, National Sci… http://dx… national, scie… <NA>
#> 2 10000… National Sleep… NSF http://dx… national, slee… United …
#> 3 10000… National Scien… USA NSF, US NSF, … http://dx… national, scie… United …
#> 4 10000… Office of the … NSF Office of the… http://dx… office, of, th… United …
#> 5 50110… National Natur… NNSF of China, NS… http://dx… national, natu… China
#> 6 10001… BioXFEL Scienc… National Science … http://dx… bioxfel, scien… United …
#> 7 50110… Norsk Sykeplei… NSF, Norwegian Nu… http://dx… norsk, sykeple… <NA>
#> 8 10000… Center for Hie… CHM, NSF, Univers… http://dx… center, for, h… United …
#> 9 10001… Kansas NSF EPS… KNE, NSF EPSCoR http://dx… kansas, nsf, e… United …
#> 10 50110… Natural Scienc… Anhui Provincial … http://dx… natural, scien… China
#> 11 10000… Statens Naturv… Danish National S… http://dx… statens, natur… <NA>
#> 12 50110… National Strok… NSF http://dx… national, stro… <NA>
#> 13 50110… NSFC-Henan Joi… NSFC-Henan Provin… http://dx… nsfc, henan, j… China
#> 14 50110… National Natur… NSFC-Yunnan Joint… http://dx… national, natu… China
#> 15 50110… National Natur… NSFC-Shandong Joi… http://dx… national, natu… China
#> 16 10001… Innovative Res… Fund for innovati… http://dx… innovative, re… China
#> 17 10001… National Outst… National Outstand… http://dx… national, outs… China
#>
#> $facets
#> NULLcr_agency(dois = '10.13039/100000001')
#> $DOI
#> [1] "10.13039/100000001"
#>
#> $agency
#> $agency$id
#> [1] "crossref"
#>
#> $agency$label
#> [1] "Crossref"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 3682545 NA 0 1
#>
#> $data
#> # A tibble: 1 x 23
#> alternative.id container.title created deposited published.online doi
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 2004-19607-00… Neuropsychology 2004-1… 2019-02-… 2004-10 10.1…
#> # … with 17 more variables: indexed <chr>, issn <chr>, issue <chr>,
#> # issued <chr>, member <chr>, page <chr>, prefix <chr>, publisher <chr>,
#> # reference.count <chr>, score <chr>, source <chr>, title <chr>, type <chr>,
#> # url <chr>, volume <chr>, author <list>, link <list>
#>
#> $facets
#> NULLcr_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… 2020-03-17 TRUE FALSE
#> 2 Jour… "America… 2326… 2020-03-11 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
#> NULLcr_licenses(query = 'elsevier')
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 38 elsevier 0 20
#>
#> $data
#> # A tibble: 38 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/ 13
#> 4 http://creativecommons.org/licenses/by-nc/4.0/ 3
#> 5 http://creativecommons.org/licenses/by/2.0 1
#> 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/ 15
#> 10 http://doi.wiley.com/10.1002/tdm_license_1 137
#> # … with 28 more rowscr_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()cr_members(query = 'ecology', limit = 5)
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 22 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>
#> 1 336 Japanese So… 5-3 Yon… 2020-03-18 1273 141
#> 2 1950 Journal of … Suite 8… 2020-03-18 0 0
#> 3 2080 The Japan S… 5-3 Yon… 2020-03-18 700 19
#> 4 2151 Ecology and… 5-3 Yon… 2020-03-18 414 37
#> 5 2169 Italian Soc… Diparti… 2020-03-18 1360 224
#> # … 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>
#>
#> $facets
#> NULLcr_r() uses the function cr_works() internally.
cr_r()
#> [1] "10.32387/prokla.v41i165.332" "10.1016/j.toxlet.2016.06.2117"
#> [3] "10.1016/s0140-6736(99)02080-2" "10.26717/bjstr.2018.02.000741"
#> [5] "10.1134/s0021364015040025" "10.1021/cen-v059n019.p006a"
#> [7] "10.2307/40147801" "10.1007/s00421-016-3378-y"
#> [9] "10.1016/j.talanta.2007.10.030" "10.1134/1.1780558"You can pass in the number of DOIs you want back (default is 10)
cr_r(2)
#> [1] "10.2307/250291" "10.2991/3ca-13.2013.9"Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at https://support.crossref.org/hc/en-us/articles/215750183-Crossref-Text-and-Data-Mining-Services
Get some DOIs for articles that provide full text, and that have CC-BY 3.0 licenses (i.e., more likely to actually be open)
out <-
cr_works(filter = list(has_full_text = TRUE,
license_url = "http://creativecommons.org/licenses/by/3.0/"))
(dois <- out$data$doi)
#> [1] "10.1016/s0370-2693(01)01497-6" "10.1016/s0370-2693(01)01503-9"
#> [3] "10.1016/s0370-2693(01)01507-6" "10.1016/s0370-2693(01)01486-1"
#> [5] "10.1016/s0370-2693(01)01512-x" "10.1016/s0370-2693(01)01518-0"
#> [7] "10.1016/s0370-2693(02)01156-5" "10.1016/s0370-2693(02)01161-9"
#> [9] "10.1016/s0370-2693(02)01162-0" "10.1016/s0370-2693(02)01163-2"
#> [11] "10.1016/s0370-2693(02)01166-8" "10.1016/s0370-2693(02)01170-x"
#> [13] "10.1016/s0370-2693(02)01174-7" "10.1016/s0370-2693(02)01179-6"
#> [15] "10.1016/s0370-2693(02)01181-4" "10.1016/s0370-2693(01)01471-x"
#> [17] "10.1016/s0370-2693(01)01473-3" "10.1016/s0370-2693(01)01467-8"
#> [19] "10.1016/s0370-2693(01)01505-2" "10.1016/s0370-2693(02)01172-3"From the output of cr_works we can get full text links if we know where to look:
do.call("rbind", out$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 rowsFrom 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.pdfThen 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: 2014-09-15See also fulltext (https://github.com/ropensci/fulltext) for getting scholarly text for text mining.
- Please report any issues or bugs: https://github.com/ropensci/rcrossref/issues
- License: MIT
- Get citation information for
rcrossrefin R doingcitation(package = 'rcrossref') - Please note that this package is released with a Contributor Code of Conduct. By contributing to 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.
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