get_organism_taxonomy_ott: Get organism taxonomy (Open Tree of Life Taxonomy)

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Get organism taxonomy (Open Tree of Life Taxonomy)

Description

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)
unlink("data", recursive = TRUE)

taxonomicallyinformedannotation/tima-r documentation built on Dec. 20, 2024, 9:32 a.m.