README
GBIF Backbone Taxonomy — Genome Gap slice
The reconciliation layer of the Revive & Restore genome gap demo. Species names are inconsistent across sources (IUCN, NCBI, zoo datasets each use different names and synonyms for the same organism). The GBIF backbone taxonomy is a synthetic classification built to cross-reference these resources, so it is the bridge that makes the join reliable rather than string-matching by hand.
This collection holds one canonical Taxon record per species in the analysis,
carrying the GBIF backbone key (nubKey), normalized higher taxonomy, the IUCN
category carried through from the checklist, and whether NCBI returned a genome
for the canonical name.
Source
- Dataset: GBIF Backbone Taxonomy, via the GBIF Species API. No key required.
- Every IUCN checklist record carries a
nubKeypointing at the backbone; this collection captures that backbone taxon plus the fields used to query NCBI.
Records
One Taxon record per species. id is gbif:{nubKey} — shared with
iucn-species and ncbi-assemblies.
Regenerate
pnpm exec tsx sources/reviverestore/scrape-genome-gap.ts
pnpm push reviverestore/gbif-backbone --env dev