An interface to the Integrated Taxonomic Information System (ITIS)
- ITIS API Docs: https://www.itis.gov/ws_description.html
- Solr service: https://www.itis.gov/solr_documentation.html
- taxize book: https://taxize.dev/
- ritis docs: https://docs.ropensci.org/ritis/
How to cite ITIS. From https://itis.gov/citation.html
To cite data obtained from ITIS, the following citation format is offered as a suggestion:
ITIS is one of many different taxonomic data sources. Other include: Catalogue of Life (and COL+), NCBI taxonomy, International Plant Names Index, Index Fungorum, and more. The Wikipedia entry (https://en.wikipedia.org/wiki/Integrated_Taxonomic_Information_System) states that ITIS has a North American focus, but includes many taxa not in North America.
Terminology
- “mononomial”: a taxonomic name with one part, e.g, Poa
- “binomial”: a taxonomic name with two parts, e.g, Poa annua
- “trinomial”: a taxonomic name with three parts, e.g, Poa annua annua
Installation
Stable, CRAN version
install.packages("ritis")
Dev version
remotes::install_github("ropensci/ritis")
The following are examples of some functions. There are many more avaiable.
Solr service
matches only monomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/") #> # A tibble: 10 x 28 #> tsn nameWInd nameWOInd unit1 usage credibilityRati… completenessRat… #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 1427… Xenocha… Xenochae… Xeno… valid TWG standards m… complete #> 2 1428… Myopiti… Myopitini Myop… inva… TWG standards m… unknown #> 3 1428… Rhynenc… Rhynenci… Rhyn… valid TWG standards m… complete #> 4 1428… Urophora Urophora Urop… valid TWG standards m… complete #> 5 1428… Oedaspi… Oedaspid… Oeda… inva… TWG standards m… unknown #> 6 1428… Aciurina Aciurina Aciu… valid TWG standards m… complete #> 7 1428… Callach… Callachna Call… inva… TWG standards m… unknown #> 8 1428… Cecidoc… Cecidoch… Ceci… valid TWG standards m… complete #> 9 1428… Eurosta Eurosta Euro… valid TWG standards m… complete #> 10 1428… Peronyma Peronyma Pero… valid TWG standards m… complete #> # … with 21 more variables: currencyRating <chr>, taxonAuthor <chr>, #> # kingdom <chr>, parentTSN <chr>, rankID <chr>, rank <chr>, #> # hierarchySoFar <chr>, hierarchySoFarWRanks <chr>, hierarchyTSN <chr>, #> # publication <chr>, otherSource <chr>, createDate <chr>, updateDate <chr>, #> # hierarchicalSort <chr>, `_version_` <dbl>, unacceptReason <chr>, #> # synonyms <chr>, synonymTSNs <chr>, acceptedTSN <chr>, comment <chr>, #> # expert <chr>
matches only binomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/") #> # A tibble: 10 x 25 #> tsn nameWInd nameWOInd unit1 unit2 usage unacceptReason credibilityRati… #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 1427… Trypeta… Trypeta … Tryp… plat… inva… original name… TWG standards m… #> 2 1427… Xenocha… Xenochae… Xeno… aura… valid <NA> TWG standards m… #> 3 1428… Eutreta… Eutreta … Eutr… aura… inva… original name… TWG standards m… #> 4 1428… Xenocha… Xenochae… Xeno… dich… valid <NA> TWG standards m… #> 5 1428… Rhynenc… Rhynenci… Rhyn… long… valid <NA> TWG standards m… #> 6 1428… Aleomyi… Aleomyia… Aleo… alpha inva… junior synonym TWG standards m… #> 7 1428… Urophor… Urophora… Urop… acut… inva… original name… TWG standards m… #> 8 1428… Urophor… Urophora… Urop… affi… valid <NA> TWG standards m… #> 9 1428… Trypeta… Trypeta … Tryp… affi… inva… original name… TWG standards m… #> 10 1428… Urophor… Urophora… Urop… card… valid <NA> TWG standards m… #> # … with 17 more variables: taxonAuthor <chr>, kingdom <chr>, rankID <chr>, #> # rank <chr>, hierarchySoFar <chr>, hierarchySoFarWRanks <chr>, #> # hierarchyTSN <chr>, synonyms <chr>, synonymTSNs <chr>, publication <chr>, #> # otherSource <chr>, acceptedTSN <chr>, createDate <chr>, updateDate <chr>, #> # `_version_` <dbl>, parentTSN <chr>, hierarchicalSort <chr>
REST API
Get accepted names for a TSN
accepted_names(tsn = 504239) #> # A tibble: 1 x 3 #> acceptedName acceptedTsn author #> <chr> <chr> <chr> #> 1 Dasiphora fruticosa 836659 (L.) Rydb.
Get common names for a TSN
common_names(tsn = 183833) #> # A tibble: 3 x 3 #> commonName language tsn #> <chr> <chr> <chr> #> 1 African hunting dog English 183833 #> 2 African Wild Dog English 183833 #> 3 Painted Hunting Dog English 183833
Full hierarchy for a TSN
hierarchy_full(tsn = 37906) #> # A tibble: 60 x 5 #> parentname parenttsn rankname taxonname tsn #> <chr> <chr> <chr> <chr> <chr> #> 1 "" "" Kingdom Plantae 202422 #> 2 "Plantae" "202422" Subkingdom Viridiplantae 954898 #> 3 "Viridiplantae" "954898" Infrakingdom Streptophyta 846494 #> 4 "Streptophyta" "846494" Superdivision Embryophyta 954900 #> 5 "Embryophyta" "954900" Division Tracheophyta 846496 #> 6 "Tracheophyta" "846496" Subdivision Spermatophytina 846504 #> 7 "Spermatophytina" "846504" Class Magnoliopsida 18063 #> 8 "Magnoliopsida" "18063" Superorder Asteranae 846535 #> 9 "Asteranae" "846535" Order Asterales 35419 #> 10 "Asterales" "35419" Family Asteraceae 35420 #> # … with 50 more rows
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
ritisin R doingcitation(package = 'ritis') - 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.