build_gbif: Rebuild the GBIF backbone snapshot

In taxadb: A High-Performance Taxonomic Database Interface

Rebuild the GBIF backbone snapshot

Description

Rebuild the GBIF backbone snapshot

Usage

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

Arguments

version	snapshot version to write, e.g. "2026"
archive	path to the GBIF backbone archive; downloaded if missing
dir	directory for build inputs and outputs
db	a duckdb connection

Details

GBIF supplies canonicalName – the name without authorship – alongside the full scientificName, so no name parsing is needed. It leaves canonicalName empty for names its parser cannot analyse, which includes the sequence-derived identifiers GBIF carries in quantity (BOLD BINs, UNITE species hypotheses, metagenome-assembled genomes) and hybrid formulas; for those the scientificName is the name, and is used.

GBIF leaves acceptedNameUsageID empty on accepted and on doubtful names alike, since it redirects neither. Both therefore become their own accepted name here, which is also what keeps GBIF's 40,895 synonyms of doubtful names resolvable.

Value

the paths written, invisibly

See Also

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

Examples

## Not run: 
build_gbif("2026")

## End(Not run)

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