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wikitaxa - Taxonomy data from Wikipedia
The goal of wikitaxa is to allow search and taxonomic data retrieval from across many Wikimedia sites, including: Wikipedia, Wikicommons, and Wikispecies.
There are lower level and higher level parts to the package API:
The low level API is meant for power users and gives you more control, but requires more knowledge.
wt_wiki_page()wt_wiki_page_parse()wt_wiki_url_build()wt_wiki_url_parse()wt_wikispecies_parse()wt_wikicommons_parse()wt_wikipedia_parse()The high level API is meant to be easier and faster to use.
wt_data()wt_data_id()wt_wikispecies()wt_wikicommons()wt_wikipedia()Search functions:
wt_wikicommons_search()wt_wikispecies_search()wt_wikipedia_search()CRAN version
install.packages("wikitaxa")Dev version
remotes::install_github("ropensci/wikitaxa")library("wikitaxa")z <- wt_data("Poa annua")
names(z)
#> [1] "labels" "descriptions" "aliases" "sitelinks" "claims"
head(z$labels)
#> language value
#> 1 pt Poa annua
#> 2 is Varpasveifgras
#> 3 pl Wiechlina roczna
#> 4 fr Pâturin annuel
#> 5 es Poa annua
#> 6 en Poa annuaGet a Wikidata ID
wt_data_id("Mimulus foliatus")
#> [1] "Q6495130"
#> attr(,"class")
#> [1] "wiki_id"lower level
pg <- wt_wiki_page("https://en.wikipedia.org/wiki/Malus_domestica")
res <- wt_wiki_page_parse(pg)
res$iwlinks
#> [1] "https://commons.wikimedia.org/wiki/Category:Apples"
#> [2] "https://commons.wikimedia.org/wiki/Category:Apple_cultivars"
#> [3] "https://www.wikidata.org/wiki/Q158657"
#> [4] "https://www.wikidata.org/wiki/Q18674606"
#> [5] "https://species.wikimedia.org/wiki/Malus_pumila"
#> [6] "https://species.wikimedia.org/wiki/Malus_domestica"higher level
res <- wt_wikipedia("Malus domestica")
res$common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Apple en
res$classification
#> # A tibble: 3 x 2
#> rank name
#> <chr> <chr>
#> 1 plainlinks ""
#> 2 binomial "Malus domestica"
#> 3 <NA> ""choose a wikipedia language
# French
wt_wikipedia(name = "Malus domestica", wiki = "fr")
#> $langlinks
#> # A tibble: 60 x 5
#> lang url langname autonym `*`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 als https://als.wikipedia.org/wiki/Kultu… Alemannis… Alemannis… Kulturapf…
#> 2 am https://am.wikipedia.org/wiki/%E1%89… amharique አማርኛ ቱፋሕ
#> 3 ast https://ast.wikipedia.org/wiki/Malus… asturien asturianu Malus dom…
#> 4 az https://az.wikipedia.org/wiki/M%C9%9… azéri azərbayca… Mədəni al…
#> 5 bat-s… https://bat-smg.wikipedia.org/wiki/V… Samogitian žemaitėška Vuobelės
#> 6 bg https://bg.wikipedia.org/wiki/%D0%94… bulgare български Домашна я…
#> 7 bpy https://bpy.wikipedia.org/wiki/%E0%A… bishnupri… বিষ্ণুপ্র… আপেল
#> 8 ca https://ca.wikipedia.org/wiki/Pomera… catalan català Pomera co…
#> 9 cs https://cs.wikipedia.org/wiki/Jablo%… tchèque čeština Jabloň do…
#> 10 csb https://csb.wikipedia.org/wiki/Dom%C… kachoube kaszëbsczi Domôcô ja…
#> # … with 50 more rows
#>
#> $externallinks
#> [1] "http://www.cabi-publishing.org/pdf/Books/0851995926/0851995926_Chap01.pdf"
#> [2] "http://www.umass.edu/fruitadvisor/fruitnotes/ontheorigin.pdf"
#> [3] "http://www.applegenome.org"
#> [4] "http://societeradio-canada.info/emissions/les_annees_lumiere/2010-2011/"
#> [5] "http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.654.html"
#> [6] "https://gallica.bnf.fr/ark:/12148/bpt6k28582v"
#> [7] "http://worldcat.org/issn/1471-2229&lang=fr"
#> [8] "https://www.ncbi.nlm.nih.gov/pubmed/26924309"
#> [9] "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4770685"
#> [10] "https://dx.doi.org/10.1186%2Fs12870-016-0739-y"
#> [11] "https://doi.org/10.1186/s12870-016-0739-y"
#> [12] "http://www.hamblenne.be/LISTE_RGF.pdf"
#> [13] "http://www.arcticapples.com/blog/john/demystifying-arctic-apples#.UaeX-Jzjmw5"
#> [14] "http://www.cctec.cornell.edu/plants/GENEVA-Apple-Rootstocks-Comparison-Chart-120911.pdf"
#> [15] "https://commons.wikimedia.org/wiki/Category:Malus_domestica?uselang=fr"
#> [16] "http://www.tela-botanica.org/page:eflore"
#> [17] "http://www.tela-botanica.org/bdtfx-nn-40744"
#> [18] "http://www.cbif.gc.ca/acp/fra/siti/regarder?tsn=516655"
#> [19] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=516655"
#> [20] "http://www.cbif.gc.ca/acp/fra/siti/regarder?tsn=25262"
#> [21] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=25262"
#> [22] "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lin=s&p=has_linkout&id=3750"
#> [23] "http://www.ars-grin.gov/"
#> [24] "https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?104681"
#> [25] "https://www.biolib.cz/en/"
#> [26] "https://www.biolib.cz/en/taxon/id39552/"
#> [27] "http://inpn.mnhn.fr/isb/espece/cd_nom/107207"
#> [28] "http://www.bmlisieux.com/normandie/roblet.htm"
#> [29] "http://site.voila.fr/babadubonsai/docum/docmal.html"
#> [30] "http://www.fruitiers.net"
#> [31] "http://www.inra.fr/hyppz/CULTURES/3c---003.htm"
#> [32] "http://cat.inist.fr/?aModele=afficheN&cpsidt=15506238"
#> [33] "http://www.omafra.gov.on.ca/french/crops/facts/98-014.htm"
#> [34] "http://www.gardenaction.co.uk/fruit_veg_diary/fruit_veg_mini_project_september_2_apple.asp"
#>
#> $common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Pommier domestique fr
#>
#> $classification
#> # A tibble: 0 x 0
#>
#> $synonyms
#> list()
# Slovak
wt_wikipedia(name = "Malus domestica", wiki = "sk")
#> $langlinks
#> # A tibble: 60 x 5
#> lang url langname autonym `*`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 als https://als.wikipedia.org/wiki/K… Alemannisch Alemannis… Kulturap…
#> 2 am https://am.wikipedia.org/wiki/%E… amharčina አማርኛ ቱፋሕ
#> 3 ast https://ast.wikipedia.org/wiki/M… astúrčina asturianu Malus do…
#> 4 az https://az.wikipedia.org/wiki/M%… azerbajdžančina azərbayca… Mədəni a…
#> 5 bat-s… https://bat-smg.wikipedia.org/wi… Samogitian žemaitėška Vuobelės
#> 6 bg https://bg.wikipedia.org/wiki/%D… bulharčina български Домашна …
#> 7 bpy https://bpy.wikipedia.org/wiki/%… bišnuprijskoma… বিষ্ণুপ্র… আপেল
#> 8 ca https://ca.wikipedia.org/wiki/Po… katalánčina català Pomera c…
#> 9 cs https://cs.wikipedia.org/wiki/Ja… čeština čeština Jabloň d…
#> 10 csb https://csb.wikipedia.org/wiki/D… kašubčina kaszëbsczi Domôcô j…
#> # … with 50 more rows
#>
#> $externallinks
#> list()
#>
#> $common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Jabloň domáca sk
#>
#> $classification
#> # A tibble: 0 x 0
#>
#> $synonyms
#> list()
# Vietnamese
wt_wikipedia(name = "Malus domestica", wiki = "vi")
#> $langlinks
#> # A tibble: 60 x 5
#> lang url langname autonym `*`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 als https://als.wikipedia.org/wiki/Kul… Alemannisch Alemanni… Kulturapf…
#> 2 am https://am.wikipedia.org/wiki/%E1%… Tiếng Amha… አማርኛ ቱፋሕ
#> 3 ast https://ast.wikipedia.org/wiki/Mal… Tiếng Astu… asturianu Malus dom…
#> 4 az https://az.wikipedia.org/wiki/M%C9… Tiếng Azer… azərbayc… Mədəni al…
#> 5 zh-min-… https://zh-min-nan.wikipedia.org/w… Chinese (M… Bân-lâm-… Phōng-kó-…
#> 6 bg https://bg.wikipedia.org/wiki/%D0%… Tiếng Bulg… български Домашна я…
#> 7 ca https://ca.wikipedia.org/wiki/Pome… Tiếng Cata… català Pomera co…
#> 8 cs https://cs.wikipedia.org/wiki/Jabl… Tiếng Séc čeština Jabloň do…
#> 9 da https://da.wikipedia.org/wiki/Almi… Tiếng Đan … dansk Almindeli…
#> 10 de https://de.wikipedia.org/wiki/Kult… Tiếng Đức Deutsch Kulturapf…
#> # … with 50 more rows
#>
#> $externallinks
#> [1] "http://biology.umaine.edu/Amelanchier/Rosaceae_2007.pdf"
#> [2] "//dx.doi.org/10.1007%2Fs00606-007-0539-9"
#> [3] "https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?410495"
#> [4] "https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?30530"
#> [5] "http://www.uga.edu/fruit/apple.html"
#> [6] "//dx.doi.org/10.3732%2Fajb.93.3.357"
#> [7] "http://www.plosgenetics.org/article/info:doi%2F10.1371%2Fjournal.pgen.1002703"
#> [8] "//www.ncbi.nlm.nih.gov/pmc/articles/PMC3349737"
#> [9] "//www.ncbi.nlm.nih.gov/pubmed/22589740"
#> [10] "//dx.doi.org/10.1371%2Fjournal.pgen.1002703"
#> [11] "http://news.sciencemag.org/sciencenow/2012/05/scienceshot-the-secret-history-o.html"
#> [12] "http://www.plantpress.com/wildlife/o523-apple.php"
#> [13] "http://cahnrsnews.wsu.edu/2010/08/29/apple-cup-rivals-contribute-to-apple-genome-sequencing/"
#> [14] "http://www.nature.com/ng/journal/v42/n10/full/ng.654.html"
#> [15] "http://www.alphagalileo.org/ViewItem.aspx?ItemId=83717&CultureCode=en"
#> [16] "http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml"
#> [17] "https://commons.wikimedia.org/wiki/Apple?uselang=vi"
#> [18] "https://commons.wikimedia.org/wiki/Category:Malus_domestica?uselang=vi"
#> [19] "http://bachkhoatoanthu.vass.gov.vn/noidung/tudien/Lists/GiaiNghia/View_Detail.aspx?ItemID=5007"
#> [20] "http://www.eol.org/pages/629094"
#> [21] "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3750"
#> [22] "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=516655"
#> [23] "http://www.catalogueoflife.org/col/details/species/id/19538828/synonym/19539435"
#> [24] "https://www.biolib.cz/cz/taxon/id39552"
#> [25] "https://gd.eppo.int/taxon/MABSD"
#> [26] "https://npgsweb.ars-grin.gov/gringlobal/taxonomydetail.aspx?id=104681"
#> [27] "http://www.ipni.org/ipni/idPlantNameSearch.do?id=726282-1"
#> [28] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=516655"
#> [29] "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3750"
#> [30] "http://www.nzor.org.nz/names/14d024a2-d821-48e3-95d8-f0dd206c70a0"
#> [31] "http://www.pfaf.org/user/Plant.aspx?LatinName=Malus+domestica"
#> [32] "http://www.theplantlist.org/tpl1.1/record/rjp-454"
#> [33] "http://www.plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:726282-1"
#> [34] "http://legacy.tropicos.org/Name/27804420"
#> [35] "https://vicflora.rbg.vic.gov.au/flora/taxon/e41b929d-b709-4f4c-8dbe-2a9241e2342b"
#> [36] "http://www.ipni.org/ipni/idPlantNameSearch.do?id=60476301-2"
#> [37] "http://www.plantsoftheworldonline.org/taxon/urn:lsid:ipni.org:names:60476301-2"
#> [38] "http://legacy.tropicos.org/Name/100473089"
#>
#> $common_names
#> # A tibble: 1 x 2
#> name language
#> <chr> <chr>
#> 1 Malus domestica vi
#>
#> $classification
#> # A tibble: 0 x 0
#>
#> $synonyms
#> list()search
wt_wikipedia_search(query = "Pinus")
#> $batchcomplete
#> [1] ""
#>
#> $continue
#> $continue$sroffset
#> [1] 10
#>
#> $continue$continue
#> [1] "-||"
#>
#>
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 3374
#>
#> $query$searchinfo$suggestion
#> [1] "penis"
#>
#> $query$searchinfo$suggestionsnippet
#> [1] "penis"
#>
#>
#> $query$search
#> # A tibble: 10 x 7
#> ns title pageid size wordcount snippet timestamp
#> <int> <chr> <int> <int> <int> <chr> <chr>
#> 1 0 Pine 39389 36555 4058 "A pine is any conifer in… 2020-06-26…
#> 2 0 Pinus po… 532941 31087 3069 "misidentified it as <spa… 2020-06-19…
#> 3 0 Pinus co… 507717 20486 2343 "all pines (member specie… 2020-05-25…
#> 4 0 Pinus je… 463015 9130 1008 "long, with a large (15 t… 2019-12-22…
#> 5 0 Pinus st… 464301 31478 3815 "3 ft) tall & wide. M… 2020-06-22…
#> 6 0 Pinus re… 507802 7501 783 ""<span class=\"sear… 2020-05-08…
#> 7 0 Pinus lo… 649634 15408 1741 "sometimes form dense for… 2020-04-14…
#> 8 0 Pinus la… 459402 11464 1338 "Fire affected this speci… 2020-01-15…
#> 9 0 Pinus ni… 438963 11947 1421 "hypodermal cells. P. nig… 2020-04-03…
#> 10 0 Pinus mu… 438946 11964 901 "encyclopedia) is still r… 2020-06-17…search supports languages
wt_wikipedia_search(query = "Pinus", wiki = "fr")
#> $batchcomplete
#> [1] ""
#>
#> $continue
#> $continue$sroffset
#> [1] 10
#>
#> $continue$continue
#> [1] "-||"
#>
#>
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 990
#>
#>
#> $query$search
#> # A tibble: 10 x 7
#> ns title pageid size wordcount snippet timestamp
#> <int> <chr> <int> <int> <int> <chr> <chr>
#> 1 0 Pin (pl… 89798 83647 9325 "<span class=\"searchmatc… 2020-05-23…
#> 2 0 Pinus p… 121544 31274 3892 "<span class=\"searchmatc… 2020-04-30…
#> 3 0 Pinus c… 98421 8237 959 "<span class=\"searchmatc… 2019-05-30…
#> 4 0 Pinus n… 950330 26623 3013 "recycler}}. <span class=… 2020-03-30…
#> 5 0 Pin syl… 121562 13725 1611 "<span class=\"searchmatc… 2020-03-22…
#> 6 0 Pinus h… 117280 22257 2671 "<span class=\"searchmatc… 2020-05-07…
#> 7 0 Pin par… 138378 8763 916 "<span class=\"searchmatc… 2020-04-26…
#> 8 0 Pinus s… 776950 11662 1628 "les articles homonymes, … 2020-04-14…
#> 9 0 Pinus m… 2480854 21747 2310 "<span class=\"searchmatc… 2019-02-25…
#> 10 0 Pinus u… 3208429 6316 720 "significations, voir Pin… 2020-03-09…lower level
pg <- wt_wiki_page("https://commons.wikimedia.org/wiki/Abelmoschus")
res <- wt_wikicommons_parse(pg)
res$common_names[1:3]
#> [[1]]
#> [[1]]$name
#> [1] "okra"
#>
#> [[1]]$language
#> [1] "en"
#>
#>
#> [[2]]
#> [[2]]$name
#> [1] "مسكي"
#>
#> [[2]]$language
#> [1] "ar"
#>
#>
#> [[3]]
#> [[3]]$name
#> [1] "Abelmoş"
#>
#> [[3]]$language
#> [1] "az"higher level
res <- wt_wikicommons("Abelmoschus")
res$classification
#> # A tibble: 15 x 2
#> rank name
#> <chr> <chr>
#> 1 Domain "Eukaryota"
#> 2 unranked "Archaeplastida"
#> 3 Regnum "Plantae"
#> 4 Cladus "angiosperms"
#> 5 Cladus "eudicots"
#> 6 Cladus "core eudicots"
#> 7 Cladus "superrosids"
#> 8 Cladus "rosids"
#> 9 Cladus "eurosids II"
#> 10 Ordo "Malvales"
#> 11 Familia "Malvaceae"
#> 12 Subfamilia "Malvoideae"
#> 13 Tribus "Hibisceae"
#> 14 Genus "Abelmoschus"
#> 15 Authority " Medik. (1787)"
res$common_names
#> # A tibble: 19 x 2
#> name language
#> <chr> <chr>
#> 1 okra en
#> 2 مسكي ar
#> 3 Abelmoş az
#> 4 Bamja bs
#> 5 Ibiškovec cs
#> 6 Bisameibisch de
#> 7 Okrat fi
#> 8 Abelmosco gl
#> 9 Abelmošus hr
#> 10 Ybiškė lt
#> 11 അബെൽമോസ്കസ് ml
#> 12 Абельмош mrj
#> 13 Abelmoskusslekta nn
#> 14 Piżmian pl
#> 15 Абельмош ru
#> 16 Okrasläktet sv
#> 17 Абельмош udm
#> 18 Chi Vông vang vi
#> 19 黄葵属 zhsearch
wt_wikicommons_search(query = "Pinus")
#> $batchcomplete
#> [1] ""
#>
#> $continue
#> $continue$sroffset
#> [1] 10
#>
#> $continue$continue
#> [1] "-||"
#>
#>
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 270
#>
#>
#> $query$search
#> # A tibble: 10 x 7
#> ns title pageid size wordcount snippet timestamp
#> <int> <chr> <int> <lgl> <int> <chr> <chr>
#> 1 0 Pinus sylvestris 9066 NA 0 "" 2020-05-13T19:…
#> 2 0 Pinus ponderosa 250435 NA 0 "" 2020-04-18T15:…
#> 3 0 Pinus nigra 64703 NA 0 "" 2018-03-06T10:…
#> 4 0 Pinus 82071 NA 0 "" 2017-05-28T10:…
#> 5 0 Pinus mugo 132442 NA 0 "" 2019-07-26T09:…
#> 6 0 Rogów Arboretum 10563490 NA 0 "" 2020-01-01T13:…
#> 7 0 Pinus contorta 186918 NA 0 "" 2020-01-19T19:…
#> 8 0 Anacortes Community F… 2989013 NA 0 "" 2014-12-10T15:…
#> 9 0 Pinus halepensis 172181 NA 0 "" 2018-05-05T10:…
#> 10 0 Pinus brutia 139389 NA 0 "" 2014-11-23T11:…lower level
pg <- wt_wiki_page("https://species.wikimedia.org/wiki/Malus_domestica")
res <- wt_wikispecies_parse(pg, types = "common_names")
res$common_names[1:3]
#> [[1]]
#> [[1]]$name
#> [1] "Ябълка"
#>
#> [[1]]$language
#> [1] "български"
#>
#>
#> [[2]]
#> [[2]]$name
#> [1] "Poma, pomera"
#>
#> [[2]]$language
#> [1] "català"
#>
#>
#> [[3]]
#> [[3]]$name
#> [1] "jabloň domácí"
#>
#> [[3]]$language
#> [1] "čeština"higher level
res <- wt_wikispecies("Malus domestica")
res$classification
#> # A tibble: 8 x 2
#> rank name
#> <chr> <chr>
#> 1 Superregnum Eukaryota
#> 2 Regnum Plantae
#> 3 Cladus Angiosperms
#> 4 Cladus Eudicots
#> 5 Cladus Core eudicots
#> 6 Cladus Rosids
#> 7 Cladus Eurosids I
#> 8 Ordo Rosales
res$common_names
#> # A tibble: 22 x 2
#> name language
#> <chr> <chr>
#> 1 Ябълка български
#> 2 Poma, pomera català
#> 3 jabloň domácí čeština
#> 4 Apfel Deutsch
#> 5 Μηλιά Ελληνικά
#> 6 Apple English
#> 7 Manzano español
#> 8 Aed-õunapuu eesti
#> 9 Tarhaomenapuu suomi
#> 10 Aapel Nordfriisk
#> # … with 12 more rowssearch
wt_wikispecies_search(query = "Pinus")
#> $batchcomplete
#> [1] ""
#>
#> $continue
#> $continue$sroffset
#> [1] 10
#>
#> $continue$continue
#> [1] "-||"
#>
#>
#> $query
#> $query$searchinfo
#> $query$searchinfo$totalhits
#> [1] 515
#>
#>
#> $query$search
#> # A tibble: 10 x 7
#> ns title pageid size wordcount snippet timestamp
#> <int> <chr> <int> <int> <int> <chr> <chr>
#> 1 0 Pinus 1.74e4 5737 784 "Familia: Pinaceae Ge… 2020-06-06…
#> 2 0 Pinus halepe… 4.51e4 4047 580 "Pinaceae Genus: <spa… 2019-12-20…
#> 3 0 Pinus pinea 4.51e4 1949 406 "Familia: Pinaceae Ge… 2019-10-19…
#> 4 0 Pinus veitch… 1.34e6 1450 181 "Familia: Pinaceae Ge… 2019-07-19…
#> 5 0 Pinus pumila 7.35e4 1395 189 "Pinaceae Genus: <spa… 2019-07-14…
#> 6 0 Pinus subg. … 3.01e5 358 27 "Pinaceae Genus: <spa… 2019-11-24…
#> 7 0 Pinus clausa 4.50e4 1552 208 "Pinaceae Genus: <spa… 2019-08-15…
#> 8 0 Pinus pseudo… 1.48e6 2114 310 "Genus: <span class=\… 2020-05-21…
#> 9 0 Pinus pinast… 1.32e6 2764 379 "Pinaceae Genus: <spa… 2019-12-20…
#> 10 0 Pinus nigra … 3.27e5 1799 138 "Genus: <span class=\… 2020-03-02…These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.