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 = {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")
#> 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] 13Search 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 100000179 United States
#> 2 501100000930 Australia
#> 3 100000001 United States
#> 4 100003187 United States
#> 5 100008367 Denmark
#> 6 501100004190 Norway
#> 7 100006445 United States
#> 8 501100001809 China
#> # ... with 4 more variables: name <chr>, alt.names <chr>, uri <chr>,
#> # tokens <chr>
#>
#> $facets
#> NULLCheck 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 688862 NA 0 1
#>
#> $data
#> # A tibble: 1 × 29
#> alternative.id container.title created deposited
#> <chr> <chr> <chr> <chr>
#> 1 1142 Regional Environmental Change 2017-03-29 2017-03-29
#> # ... with 25 more variables: DOI <chr>, funder <list>, indexed <chr>,
#> # ISBN <chr>, ISSN <chr>, issued <chr>, license_date <chr>,
#> # license_URL <chr>, license_delay.in.days <chr>,
#> # license_content.version <chr>, link <list>, member <chr>,
#> # prefix <chr>, publisher <chr>, reference.count <chr>, score <chr>,
#> # source <chr>, subject <chr>, title <chr>, type <chr>,
#> # update.policy <chr>, URL <chr>, assertion <list>, author <list>,
#> # `clinical-trial-number` <list>
#>
#> $facets
#> NULLSearch journals
cr_journals(issn = c('1803-2427','2326-4225'))
#> $data
#> # 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>
#>
#> $facets
#> NULLSearch license information
cr_licenses(query = 'elsevier')
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 17 elsevier 0 20
#>
#> $data
#> # A tibble: 17 × 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/3.0/
#> 4 http://creativecommons.org/licenses/by/4.0
#> 5 http://creativecommons.org/licenses/by/4.0/
#> 6 http://doi.wiley.com/10.1002/tdm_license_1
#> 7 http://doi.wiley.com/10.1002/tdm_license_1.1
#> 8 http://journals.iucr.org/services/copyrightpolicy.html
#> 9 http://journals.iucr.org/services/copyrightpolicy.html#TDM
#> 10 http://onlinelibrary.wiley.com/termsAndConditions
#> 11 http://www.acm.org/publications/policies/copyright_policy#Background
#> 12 http://www.bioone.org/page/resources/researchers/rights_and_permissions
#> 13 http://www.elsevier.com/open-access/userlicense/1.0/
#> 14 http://www.elsevier.com/tdm/userlicense/1.0/
#> 15 http://www.emeraldinsight.com/page/tdm
#> 16 http://www.springer.com/tdm
#> 17 © 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>, total.dois <chr>, current.dois <chr>,
#> # backfile.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>
#>
#> $facets
#> NULLGet N random DOIs
cr_r() uses the function cr_works() internally.
cr_r()
#> [1] "10.1007/s10841-016-9867-9"
#> [2] "10.1016/b978-1-4557-3383-5.00008-7"
#> [3] "10.1515/9783110953527-fm"
#> [4] "10.1007/bf01571686"
#> [5] "10.1002/chin.201027234"
#> [6] "10.1002/9780470872864.ch23"
#> [7] "10.1090/s0273-0979-1992-00325-7"
#> [8] "10.1016/j.ejphar.2007.05.027"
#> [9] "10.1111/j.1538-7836.2005.01695.x"
#> [10] "10.1109/wisnet.2012.6172160"You can pass in the number of DOIs you want back (default is 10)
cr_r(2)
#> [1] "10.1007/bf02256554" "10.2307/3467745"Get full text
Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at http://tdmsupport.crossref.org/.
Get some DOIs for articles that provide full text, and that have CC-BY 3.0 licenses (i.e., more likely to actually be open)
out <-
cr_works(filter = list(has_full_text = TRUE,
license_url = "http://creativecommons.org/licenses/by/3.0/"))
(dois <- out$data$DOI)
#> [1] "10.1093/ecam/nem168" "10.1016/j.mri.2010.09.002"
#> [3] "10.1016/j.stem.2009.11.001" "10.1016/j.cellsig.2011.08.019"
#> [5] "10.1016/j.physletb.2011.09.006" "10.1155/2008/424320"
#> [7] "10.1155/2008/496467" "10.1155/2008/345478"
#> [9] "10.1155/2009/730902" "10.1155/2009/625469"
#> [11] "10.1155/2008/195873" "10.1016/j.physletb.2011.09.011"
#> [13] "10.1016/j.dnarep.2012.04.002" "10.1016/j.meegid.2008.11.006"
#> [15] "10.1016/j.physletb.2011.09.010" "10.4061/2010/478746"
#> [17] "10.4061/2010/348919" "10.1016/j.adhoc.2012.03.013"
#> [19] "10.1155/2011/124595" "10.1016/j.molcel.2007.09.005"From the output of cr_works we can get full text links if we know where to look:
do.call("rbind", out$data$link)
#> # A tibble: 39 × 4
#> URL
#> <chr>
#> 1 http://downloads.hindawi.com/journals/ecam/2010/174726.pdf
#> 2 http://api.elsevier.com/content/article/PII:S0730725X10002742?httpAccept=te
#> 3 http://api.elsevier.com/content/article/PII:S0730725X10002742?httpAccept=te
#> 4 http://api.elsevier.com/content/article/PII:S1934590909005748?httpAccept=te
#> 5 http://api.elsevier.com/content/article/PII:S1934590909005748?httpAccept=te
#> 6 http://api.elsevier.com/content/article/PII:S0898656811002658?httpAccept=te
#> 7 http://api.elsevier.com/content/article/PII:S0898656811002658?httpAccept=te
#> 8 http://api.elsevier.com/content/article/PII:S0370269311010689?httpAccept=te
#> 9 http://api.elsevier.com/content/article/PII:S0370269311010689?httpAccept=te
#> 10 http://downloads.hindawi.com/journals/ijmms/2008/424320.pdf
#> # ... with 29 more rows, and 3 more variables: content.type <chr>,
#> # content.version <chr>, intended.application <chr>From there, you can grab your full text, but because most links require
authentication, enter another package: crminer.
Get full text
You'll need package crminer for the rest
Onc we have DOIs, get URLs to full text content
if (!requireNamespace("crminer")) {
install.packages("crminer")
}library(crminer)
(links <- crm_links(dois[1]))
#> $pdf
#> <url> http://downloads.hindawi.com/journals/ecam/2010/174726.pdfThen use those URLs to get full text
crm_pdf(links)
#> <document>/Users/sacmac/Library/Caches/crminer/174726.pdf
#> Pages: 7
#> No. characters: 36232
#> Created: 2014-03-26See also fulltext for getting scholarly text for text mining.
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
rcrossrefin R doingcitation(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.
