README
NCBI Genome Assemblies (vertebrates)
Reference genome assembly metadata from NCBI Datasets, matched to the
IUCN-assessed vertebrate species in reviverestore/iucn-species. This is the
"has a reference genome" axis of the genome gap: paired with the IUCN status, it
answers the killer question at any slice — how many species, at a given threat
level, have a reference genome?
Only assembly metadata is stored (accession, level, RefSeq category, dates, taxonomy) — never the sequences themselves, which keeps the collection small.
Source
- API: NCBI Datasets v2 —
genome/taxon/{name}/dataset_report, queried by the GBIF canonical name of each threatened species. - Rate limits: 5 requests/second without an API key, 10/second with one
(set
NCBI_API_KEY). - A species with no assembly (or absent from NCBI taxonomy) simply produces no records here — that absence is the gap, computed at the app level.
Records
One Assembly record per genome assembly. id is the NCBI accession. Each record
carries gbifKey (the GBIF backbone key of the species it was matched to) so it
joins to iucn-species and gbif-backbone.
Regenerate
pnpm exec tsx sources/reviverestore/scrape-genome-gap.ts
pnpm push reviverestore/ncbi-assemblies --env dev