Get organism taxonomy (Open Tree of Life Taxonomy)

This function retrieves taxonomy from the Open Tree of Life taxonomy

Usage

get_organism_taxonomy_ott(
  df,
  url = "https://api.opentreeoflife.org/v3/taxonomy/about",
  retry = TRUE
)

Arguments

df

Dataframe containing your organism(s) name(s)

url

url of the ott api (for testing purposes)

retry

Boolean. Retry with generic epithet

Value

The path to the obtained OTT taxonomy

Examples

df <- data.frame("organism" = "Homo sapiens")
get_organism_taxonomy_ott(df)
#> 2024-12-18 14:28:19 Testing if Open Tree of Life API is up 
#> 2024-12-18 14:28:20 Success! Submitting request... 
#> 2024-12-18 14:28:21 Request finished! 
#> 2024-12-18 14:28:21 Getting taxonomy... 
#> 2024-12-18 14:28:21 Taxonomy retrieved! 
#> 2024-12-18 14:28:21 Got OTTaxonomy! 
#>    organism_name organism_taxonomy_ottid organism_taxonomy_01domain
#>           <char>                   <int>                     <char>
#> 1:  Homo sapiens                  770315                  Eukaryota
#>    organism_taxonomy_02kingdom organism_taxonomy_03phylum
#>                         <char>                     <char>
#> 1:                     Metazoa                   Chordata
#>    organism_taxonomy_04class organism_taxonomy_06family
#>                       <char>                     <char>
#> 1:                  Mammalia                  Hominidae
#>    organism_taxonomy_08genus organism_taxonomy_09species
#>                       <char>                      <char>
#> 1:                      Homo                Homo sapiens
#>    organism_taxonomy_05order organism_taxonomy_07tribe
#>                       <char>                    <char>
#> 1:                      <NA>                      <NA>
#>    organism_taxonomy_10varietas
#>                          <char>
#> 1:                         <NA>
unlink("data", recursive = TRUE)