Get Citoid data

cit_oid(id, format = "mediawiki", accept_language = NULL, ...)

cit_oid_(id, format = "mediawiki", accept_language = NULL, ...)

Arguments

id

(character) id of an article, DOI, ISBN, PMCID or PMID

format

(character) the format to use for the resulting citation data. one of mediawiki (default), zotero, mediawiki-basefields, bibtex

accept_language

(character) for some articles the result depends on the accept language value, so provide it if localized content is required

...

curl options passed on to crul::verb-GET

Value

list of lists or character, see http://opencitations.net/index/coci/api/v1 for explanation of the resulting columns

Details

cit_oid_() gets raw text (either bibtex or JSON), and cit_oid() parses the text as appropriate for the type

References

https://en.wikipedia.org/api/rest_v1/#!/Citation/getCitation, https://www.mediawiki.org/wiki/Citoid

Examples

url<-"https://en.wikipedia.org/api/rest_v1/data/citation/mediawiki/30446726" if (crul::ok(url)) { pmid1 <- 30446726 cit_oid(pmid1) }
#> [[1]] #> [[1]]$key #> [1] "TXF3E7XU" #> #> [[1]]$version #> [1] 0 #> #> [[1]]$itemType #> [1] "journalArticle" #> #> [[1]]$tags #> [[1]]$tags[[1]] #> [[1]]$tags[[1]]$tag #> [1] "Animals" #> #> [[1]]$tags[[1]]$type #> [1] 1 #> #> #> [[1]]$tags[[2]] #> [[1]]$tags[[2]]$tag #> [1] "Antigen Presentation" #> #> [[1]]$tags[[2]]$type #> [1] 1 #> #> #> [[1]]$tags[[3]] #> [[1]]$tags[[3]]$tag #> [1] "Antigens" #> #> [[1]]$tags[[3]]$type #> [1] 1 #> #> #> [[1]]$tags[[4]] #> [[1]]$tags[[4]]$tag #> [1] "CD4-Positive T-Lymphocytes" #> #> [[1]]$tags[[4]]$type #> [1] 1 #> #> #> [[1]]$tags[[5]] #> [[1]]$tags[[5]]$tag #> [1] "Cell Proliferation" #> #> [[1]]$tags[[5]]$type #> [1] 1 #> #> #> [[1]]$tags[[6]] #> [[1]]$tags[[6]]$tag #> [1] "Cells, Cultured" #> #> [[1]]$tags[[6]]$type #> [1] 1 #> #> #> [[1]]$tags[[7]] #> [[1]]$tags[[7]]$tag #> [1] "Coculture Techniques" #> #> [[1]]$tags[[7]]$type #> [1] 1 #> #> #> [[1]]$tags[[8]] #> [[1]]$tags[[8]]$tag #> [1] "Female" #> #> [[1]]$tags[[8]]$type #> [1] 1 #> #> #> [[1]]$tags[[9]] #> [[1]]$tags[[9]]$tag #> [1] "Humans" #> #> [[1]]$tags[[9]]$type #> [1] 1 #> #> #> [[1]]$tags[[10]] #> [[1]]$tags[[10]]$tag #> [1] "Lung" #> #> [[1]]$tags[[10]]$type #> [1] 1 #> #> #> [[1]]$tags[[11]] #> [[1]]$tags[[11]]$tag #> [1] "Mice" #> #> [[1]]$tags[[11]]$type #> [1] 1 #> #> #> [[1]]$tags[[12]] #> [[1]]$tags[[12]]$tag #> [1] "Mice, Inbred BALB C" #> #> [[1]]$tags[[12]]$type #> [1] 1 #> #> #> [[1]]$tags[[13]] #> [[1]]$tags[[13]]$tag #> [1] "Mucous Membrane" #> #> [[1]]$tags[[13]]$type #> [1] 1 #> #> #> [[1]]$tags[[14]] #> [[1]]$tags[[14]]$tag #> [1] "Mycobacterium bovis" #> #> [[1]]$tags[[14]]$type #> [1] 1 #> #> #> [[1]]$tags[[15]] #> [[1]]$tags[[15]]$tag #> [1] "Mycobacterium tuberculosis" #> #> [[1]]$tags[[15]]$type #> [1] 1 #> #> #> [[1]]$tags[[16]] #> [[1]]$tags[[16]]$tag #> [1] "Programmed Cell Death 1 Receptor" #> #> [[1]]$tags[[16]]$type #> [1] 1 #> #> #> [[1]]$tags[[17]] #> [[1]]$tags[[17]]$tag #> [1] "Receptors, Immunologic" #> #> [[1]]$tags[[17]]$type #> [1] 1 #> #> #> [[1]]$tags[[18]] #> [[1]]$tags[[18]]$tag #> [1] "Tuberculosis" #> #> [[1]]$tags[[18]]$type #> [1] 1 #> #> #> [[1]]$tags[[19]] #> [[1]]$tags[[19]]$tag #> [1] "Tuberculosis Vaccines" #> #> [[1]]$tags[[19]]$type #> [1] 1 #> #> #> [[1]]$tags[[20]] #> [[1]]$tags[[20]]$tag #> [1] "Vaccination" #> #> [[1]]$tags[[20]]$type #> [1] 1 #> #> #> #> [[1]]$title #> [1] "Enhanced protection conferred by mucosal BCG vaccination associates with presence of antigen-specific lung tissue-resident PD-1+ KLRG1- CD4+ T cells" #> #> [[1]]$pages #> [1] "555–564" #> #> [[1]]$ISSN #> [[1]]$ISSN[[1]] #> [1] "1935-3456" #> #> #> [[1]]$journalAbbreviation #> [1] "Mucosal Immunol" #> #> [[1]]$publicationTitle #> [1] "Mucosal Immunology" #> #> [[1]]$volume #> [1] "12" #> #> [[1]]$issue #> [1] "2" #> #> [[1]]$date #> [1] "03 2019" #> #> [[1]]$abstractNote #> [1] "BCG, the only vaccine licensed against tuberculosis, demonstrates variable efficacy in humans. Recent preclinical studies highlight the potential for mucosal BCG vaccination to improve protection. Lung tissue-resident memory T cells reside within the parenchyma, potentially playing an important role in protective immunity to tuberculosis. We hypothesised that mucosal BCG vaccination may enhance generation of lung tissue-resident T cells, affording improved protection against Mycobacterium tuberculosis. In a mouse model, mucosal intranasal (IN) BCG vaccination conferred superior protection in the lungs compared to the systemic intradermal (ID) route. Intravascular staining allowed discrimination of lung tissue-resident CD4+ T cells from those in the lung vasculature, revealing that mucosal vaccination resulted in an increased frequency of antigen-specific tissue-resident CD4+ T cells compared to systemic vaccination. Tissue-resident CD4+ T cells induced by mucosal BCG displayed enhanced proliferative capacity compared to lung vascular and splenic CD4+ T cells. Only mucosal BCG induced antigen-specific tissue-resident T cells expressing a PD-1+ KLRG1- cell-surface phenotype. These cells constitute a BCG-induced population which may be responsible for the enhanced protection observed with IN vaccination. We demonstrate that mucosal BCG vaccination significantly improves protection over systemic BCG and this correlates with a novel population of BCG-induced lung tissue-resident CD4+ T cells." #> #> [[1]]$DOI #> [1] "10.1038/s41385-018-0109-1" #> #> [[1]]$extra #> [1] "PMID: 30446726\nPMCID: PMC7051908" #> #> [[1]]$libraryCatalog #> [1] "PubMed" #> #> [[1]]$url #> [1] "https://pubmed.ncbi.nlm.nih.gov/30446726" #> #> [[1]]$accessDate #> [1] "2020-11-21" #> #> [[1]]$author #> [[1]]$author[[1]] #> [[1]]$author[[1]][[1]] #> [1] "N. C." #> #> [[1]]$author[[1]][[2]] #> [1] "Bull" #> #> #> [[1]]$author[[2]] #> [[1]]$author[[2]][[1]] #> [1] "E." #> #> [[1]]$author[[2]][[2]] #> [1] "Stylianou" #> #> #> [[1]]$author[[3]] #> [[1]]$author[[3]][[1]] #> [1] "D. A." #> #> [[1]]$author[[3]][[2]] #> [1] "Kaveh" #> #> #> [[1]]$author[[4]] #> [[1]]$author[[4]][[1]] #> [1] "N." #> #> [[1]]$author[[4]][[2]] #> [1] "Pinpathomrat" #> #> #> [[1]]$author[[5]] #> [[1]]$author[[5]][[1]] #> [1] "J." #> #> [[1]]$author[[5]][[2]] #> [1] "Pasricha" #> #> #> [[1]]$author[[6]] #> [[1]]$author[[6]][[1]] #> [1] "R." #> #> [[1]]$author[[6]][[2]] #> [1] "Harrington-Kandt" #> #> #> [[1]]$author[[7]] #> [[1]]$author[[7]][[1]] #> [1] "M. C." #> #> [[1]]$author[[7]][[2]] #> [1] "Garcia-Pelayo" #> #> #> [[1]]$author[[8]] #> [[1]]$author[[8]][[1]] #> [1] "P. J." #> #> [[1]]$author[[8]][[2]] #> [1] "Hogarth" #> #> #> [[1]]$author[[9]] #> [[1]]$author[[9]][[1]] #> [1] "H." #> #> [[1]]$author[[9]][[2]] #> [1] "McShane" #> #> #> #> [[1]]$PMID #> [1] "30446726" #> #> [[1]]$PMCID #> [1] "7051908" #> #> [[1]]$source #> [[1]]$source[[1]] #> [1] "PubMed" #> #> [[1]]$source[[2]] #> [1] "Zotero" #> #> #>
if (FALSE) { doi1 <- "10.1108/jd-12-2013-0166" doi2 <- "10.1371/journal.pone.0058568" pmid1 <- 30446726 pmcid1 <- "PMC4679344" isbn1 <- 1439895619 # different formats cit_oid(doi1) cit_oid(pmid1, format = "mediawiki") cit_oid(pmid1, format = "zotero") cit_oid(pmid1, format = "mediawiki-basefields") cat(cit_oid(pmid1, format = "bibtex")[[1]]) # PMID example cit_oid(pmid1, verbose = TRUE) # ISBN example cit_oid(isbn1, verbose = TRUE) # PMCID example cit_oid(pmcid1) # set the accept language x <- cit_oid(pmid1, accept_language = "fr-FR", verbose = TRUE) x <- cit_oid(doi2, accept_language = "de-DE", verbose = TRUE) # just get raw text/json cit_oid_(pmcid1) # many ids at once cit_oid(id = c(pmid1, pmcid1, isbn1)) cit_oid_(id = c(pmid1, pmcid1, isbn1)) cit_oid_(id = c(pmid1, pmcid1, isbn1), format = "bibtex") }