An interface to the Integrated Taxonomic Information System (ITIS)
See also the taxize book (https://taxize.dev/) for a manual on working with taxonomic data in R, including with ITIS data.
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:
Retrieved [month, day, year], from the Integrated Taxonomic Information System on-line database, http://www.itis.gov.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
Install from CRAN
install.packages("ritis")Or install the development version from GitHub
remotes::install_github("ropensci/ritis")Load ritis
ITIS Solr interface
There are four methods.
-
itis_search()- Search -
itis_group()- Group -
itis_highlight()- Hightlight -
itis_facet()- Facet
These four methods use the equivalent functions in the package
solrium, e.g., ritis::itis_search() uses
solrium::solr_search(), etc. The itis_*()
functions simply use ... to allow users to pass on
parameters to the wrapped solrium functions. So do read the
solrium docs.
ITIS Solr API docs: https://www.itis.gov/solr_documentation.html
Some examples:
matches only monomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/")
#> # A tibble: 10 x 25
#> tsn nameWInd nameWOInd unit1 usage credibilityRati… completenessRat…
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1526… Ornitho… Ornithoi… Orni… valid No review; untr… unknown
#> 2 1526… Ornitho… Ornithoc… Orni… valid No review; untr… unknown
#> 3 1526… Ornitho… Ornithom… Orni… valid No review; untr… unknown
#> 4 1526… Pseudol… Pseudoly… Pseu… valid No review; untr… unknown
#> 5 1527… Stilbom… Stilbome… Stil… valid No review; untr… unknown
#> 6 1527… Nycteri… Nycterib… Nyct… valid No review; untr… unknown
#> 7 1527… Nycteri… Nycterib… Nyct… inva… No review; untr… unknown
#> 8 1527… Nycteri… Nycterib… Nyct… valid No review; untr… unknown
#> 9 1527… Basilia Basilia Basi… valid No review; untr… unknown
#> 10 1527… Strebli… Streblin… Stre… valid No review; untr… unknown
#> # … with 18 more variables: currencyRating <chr>, kingdom <chr>,
#> # parentTSN <chr>, rankID <chr>, rank <chr>, hierarchySoFar <chr>,
#> # hierarchySoFarWRanks <chr>, hierarchyTSN <chr>, otherSource <chr>,
#> # createDate <chr>, updateDate <chr>, hierarchicalSort <chr>,
#> # `_version_` <dbl>, synonyms <chr>, synonymTSNs <chr>, vernacular <chr>,
#> # unacceptReason <chr>, acceptedTSN <chr>matches only binomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/")
#> # A tibble: 10 x 24
#> tsn nameWInd nameWOInd unit1 unit2 usage unacceptReason credibilityRati…
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 1526… Feronia… Feronia … Fero… spin… inva… junior synonym No review; untr…
#> 2 1526… Ornitho… Ornithoi… Orni… conf… valid <NA> No review; untr…
#> 3 1526… Ornitho… Ornithom… Orni… conf… inva… junior synonym No review; untr…
#> 4 1526… Ornitho… Ornithoi… Orni… vici… valid <NA> No review; untr…
#> 5 1526… Ornitho… Ornithoi… Orni… prom… inva… junior synonym No review; untr…
#> 6 1526… Ornitho… Ornithom… Orni… vici… inva… junior synonym No review; untr…
#> 7 1526… Ornitho… Ornithoc… Orni… eryt… valid <NA> No review; untr…
#> 8 1526… Ornitho… Ornithom… Orni… bute… inva… junior synonym No review; untr…
#> 9 1526… Ornitho… Ornithom… Orni… eryt… inva… junior synonym No review; untr…
#> 10 1526… Ornitho… Ornithom… Orni… nebu… inva… junior synonym No review; untr…
#> # … with 16 more variables: taxonAuthor <chr>, kingdom <chr>, rankID <chr>,
#> # rank <chr>, hierarchySoFar <chr>, hierarchySoFarWRanks <chr>,
#> # hierarchyTSN <chr>, synonyms <chr>, synonymTSNs <chr>, otherSource <chr>,
#> # acceptedTSN <chr>, createDate <chr>, updateDate <chr>, `_version_` <dbl>,
#> # parentTSN <chr>, hierarchicalSort <chr>The syntax for itis_search() can be a bit hard to grasp.
See this ITIS page https://itis.gov/solr_examples.html for help on
generating the syntax they want for specific searches.
ITIS REST API interface
ITIS REST API docs: http://www.itis.gov/ws_description.html
The following are some example uses. There are many more methods not shown below
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 183833Full 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