build_ott: Rebuild the Open Tree Taxonomy snapshot

In taxadb: A High-Performance Taxonomic Database Interface

Rebuild the Open Tree Taxonomy snapshot

Description

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

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.

Value

the paths written, invisibly

See Also

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

Examples

## Not run: 
build_ott("2026")

## End(Not run)

taxadb documentation built on Aug. 31, 2026, 5:07 p.m.