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)." <URL: http://doi.org/10.6084/m9.figshare.97218>,
#> <URL: http://dx.doi.org/10.6084/m9.figshare.97218>.Citation count
Citation count, using OpenURL
cr_citation_count(doi = "10.1371/journal.pone.0042793")
#> [1] 7Search Crossref metadata API
The following functions all use the CrossRef API.
Look up funder information
cr_fundref(query = "NSF")
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 8 NSF 0 20
#>
#> $data
#> Source: local data frame [8 x 6]
#>
#> id location
#> (chr) (chr)
#> 1 501100000930 Australia
#> 2 100000001 United States
#> 3 100003187 United States
#> 4 100008367 Denmark
#> 5 501100004190 Norway
#> 6 100000179 United States
#> 7 100006445 United States
#> 8 501100001809 China
#> Variables not shown: 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 254101 NA 0 1
#>
#> $data
#> Source: local data frame [1 x 23]
#>
#> alternative.id container.title created deposited
#> (chr) (chr) (chr) (chr)
#> 1 2015-11-11 2015-11-11
#> Variables not shown: DOI (chr), funder (chr), indexed (chr), ISBN (chr),
#> ISSN (chr), issued (chr), link (chr), member (chr), prefix (chr),
#> publisher (chr), reference.count (chr), score (chr), source (chr),
#> subject (chr), title (chr), type (chr), URL (chr), assertion (chr),
#> author (chr)
#>
#> $facets
#> NULLSearch journals
cr_journals(issn = c('1803-2427','2326-4225'))
#> Source: local data frame [2 x 15]
#>
#> alternative.id container.title created deposited funder indexed ISBN
#> (chr) (chr) (chr) (chr) (chr) (chr) (chr)
#> 1 <NULL>
#> 2 <NULL>
#> Variables not shown: ISSN (chr), issued (chr), link (chr), publisher
#> (chr), subject (chr), title (chr), assertion (chr), author (chr)Search license information
cr_licenses(query = 'elsevier')
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 11 elsevier 0 20
#>
#> $data
#> Source: local data frame [11 x 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://doi.wiley.com/10.1002/tdm_license_1
#> 5 http://onlinelibrary.wiley.com/termsAndConditions
#> 6 http://www.acm.org/publications/policies/copyright_policy#Background
#> 7 http://www.elsevier.com/open-access/userlicense/1.0/
#> 8 http://www.elsevier.com/tdm/userlicense/1.0/
#> 9 http://www.springer.com/tdm
#> 10 © 2007 Elsevier Masson SAS. All rights reserved. The patient figure in Figu
#> 11 © 2012, Elsevier Inc., All Rights Reserved. Figure 8, part (B) (images of H
#> Variables not shown: 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
#> Source: local data frame [5 x 3]
#>
#> member name
#> (chr) (chr)
#> 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 + Business Media
#> 4 http://id.crossref.org/member/1989 Co-Action Publishing
#> 5 http://id.crossref.org/member/286 Oxford University Press (OUP)
#> Variables not shown: prefix (chr)
#>
#> $facets
#> list()Search CrossRef members
cr_members(query = 'ecology', limit = 5)
#> $meta
#> total_results search_terms start_index items_per_page
#> 1 17 ecology 0 5
#>
#> $data
#> Source: local data frame [5 x 40]
#>
#> id primary_name
#> (int) (chr)
#> 1 7052 Chinese Journal of Plant Ecology
#> 2 6933 Knowledge Ecology International
#> 3 7278 Korean Society of Ecology and Infrastructure Engineering
#> 4 7745 Institute of Applied Ecology
#> 5 336 Japanese Society of Microbial Ecology
#> Variables not shown: location (chr), last_status_check_time (date),
#> backfile.dois (chr), current.dois (chr), total.dois (chr), prefixes
#> (chr), coverge.funders.backfile (chr), coverge.licenses.backfile (chr),
#> coverge.funders.current (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.resource.links.current (chr), coverge.references.current
#> (chr), flags.deposits.orcids.current (chr), flags.deposits (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.funders.current (chr),
#> flags.deposits.references.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)
#>
#> $facets
#> NULLGet N random DOIs
cr_r() uses the function cr_works() internally.
cr_r()
#> [1] "10.5594/j16363" "10.1093/icsidreview/23.1.164"
#> [3] "10.1007/bf03302528" "10.1163/1877-8054_cmri_com_24648"
#> [5] "10.1080/08911916.1996.11643918" "10.1007/978-94-011-1472-1_34"
#> [7] "10.4267/10608/4227" "10.1103/physrevd.36.527"
#> [9] "10.1002/pam.20136" "10.1016/j.ijleo.2015.09.110"You can pass in the number of DOIs you want back (default is 10)
cr_r(2)
#> [1] "10.1201/b19172-3" "10.4236/msce.2013.15009"pmid2doi & doi2pmid
DOIs to PMIDs
UPDATE: as of 2014-12-23 the web API behind these functions is down - we'll update the package once the API is up again
Get full text links to works
Publishers can optionally provide links in the metadata they provide to Crossref for full text of the work, but that data is often missing. Find out more about it at http://tdmsupport.crossref.org/.
Get some DOIs for articles that provide full text, and that have CC-BY 3.0 licenses (i.e., more likely to actually be open)
out <-
cr_works(filter = list(has_full_text = TRUE,
license_url = "http://creativecommons.org/licenses/by/3.0/"))
(dois <- out$data$DOI)
#> [1] "10.1155/2015/108274" "10.1016/j.susc.2014.02.008"
#> [3] "10.1155/2014/152487" "10.1016/j.susc.2014.03.018"
#> [5] "10.1155/2014/101496" "10.1155/2014/156438"
#> [7] "10.1155/1989/60313" "10.1155/2008/683505"
#> [9] "10.1155/2009/867380" "10.1155/2009/316249"
#> [11] "10.4061/2010/147142" "10.1155/2010/285376"
#> [13] "10.5402/2011/736062" "10.1155/2011/434375"
#> [15] "10.1155/2011/891593" "10.1155/2010/282464"
#> [17] "10.1155/2011/875028" "10.1155/2011/463704"
#> [19] "10.1155/2011/129341" "10.1155/2011/814794"Then get URLs to full text content
(links <- cr_ft_links(dois[1]))
#> <url> http://downloads.hindawi.com/journals/cmmm/2015/108274.xmlThen 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>
#> .................... cutoffMeta
- 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.