In ropensci/ritis: Integrated Taxonomic Information System Client

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

library("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  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