Build the species catalog record (taxa.json)

One entry per taxon of the release's taxon table with an observation at or below it — the observed taxa plus their ancestors — with its lineage, the ids, the groups it belongs to, its direct and rolled-up observation counts, and one block per dataset that observed it carrying that dataset's own name for it. The 204 vocabulary-only rows of v2026.09.06 get no entry: they are listed under their dataset in datasets[].vocabulary_only[].

Usage

build_taxa_catalog(con, record, release_version = NULL, release_date = NULL)

Arguments

con

a DBI connection holding the release tables taxon, dataset_taxon, taxon_group and obs_bio (and, optionally, dataset)

record

the datasets.json record — a path or the list from build_dataset_catalog() — read for datasets[].dataset_name_short, color and category, and for the catalog order of datasets[]

release_version

the release version (default: the record's)

release_date

the release date, YYYY-MM-DD (default: the record's)

Value

A list ready for write_taxa_catalog() / jsonlite::write_json(auto_unbox = TRUE), validating against inst/schema/taxa.schema.json.

Details

Everything is read from the release: taxon, dataset_taxon, taxon_group and obs_bio on con, the dataset names, colours and categories from record (the datasets.json the release has just written, so the dots on a species page and on a dataset page cannot disagree). Nothing is authored and nothing is fetched.

Six grouped queries do the counting and every per-taxon lookup is a split index, so the builder is linear in the number of obs_bio groups, not quadratic in the number of taxa.

See also

write_taxa_catalog(), validate_taxa_catalog(), check_taxa_catalog()