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Rebuild the Open Tree Taxonomy snapshot

Source: R/build_ott.R
build_ott.Rd

Rebuild the Open Tree Taxonomy snapshot

Usage

build_ott(
  version = format(Sys.Date(), "%Y"),
  archive = NULL,
  ott_version = "3.7.3",
  dir = build_dir(),
  db = td_connect()
)

Arguments

version

snapshot version to write, e.g. "2026"

archive

path to the OTT release archive; downloaded if missing

ott_version

the OTT release to build from, e.g. "3.7.3"

dir

directory for build inputs and outputs

db

a duckdb connection

Value

the paths written, invisibly

Details

OTT ships taxonomy.tsv and synonyms.tsv, both delimited with \\t|\\t. synonyms.tsv keys each synonym to the uid of the name it is a synonym of: OTT mints no identifier for the synonym itself, so those rows carry a NULL taxonID, which the taxadb rules allow.

OTT no longer populates the type column of synonyms.tsv – it is empty for all 2.2 million rows in release 3.7.3 – so a synonym is recorded as synonym unless a type is given.

OTT publishes no vernacular names, so there is no common table for this provider; filter_common() warns accordingly.

See also

Other build: build_col(), build_fishbase(), build_gbif(), build_itis(), build_ncbi()

Examples

if (FALSE) { # \dontrun{
build_ott("2026")
} # }