omnilab / gbif

1.x-dev 2026-10-15 01:49 UTC

Requires

• php: >=8.2
• glitchr/omnilab: ^1.0@dev
• symfony/http-client: ^6.4|^7.0|^8.0

Requires (Dev)

• phpunit/phpunit: ^11.0

MIT

• Marco Meyer

• taxonomy
• science
• species
• gbif
• omnilab
• biodiversity
• catalogue-of-life

Published on Packagist.org on 2026-10-15 02:15 UTC

README

GBIF's taxonomy for glitchr/omnilab: a taxon by its key, by its legacy GBIF Backbone number, by its NCBI Taxonomy id or by a scientific name GBIF matches; its name, authority, rank, taxonomic status, IUCN Red List category, common name, place of publication and classification; its legacy number and its NCBI id as cross-references for the Collector to follow, its parent (or, for a synonym, its accepted taxon) as a related thing; a search of GBIF's names. Through the GBIF API, no key.

Since June 2026 GBIF's taxonomy is the Catalogue of Life eXtended Release, whose keys are short and alphanumeric (4CGXP for the lion); the GBIF Backbone it replaces, frozen since 2023, numbered its taxa (5219404, the same lion), and most of the world still cites those numbers (Wikidata's P846, NCBI's links). The source answers with the new key and gives the legacy number beside it; the core's gbif scheme reads both.

$gbif = (new GbifSourceFactory($http))->create(['mailto' => '[e-mail]']);
$lion = $gbif->entity('4CGXP');                  // or '5219404', 'gbif:4CGXP', 'Panthera leo', 'Felis leo', 'taxonomy:9689'
$lion->label;                                    // Panthera leo
$lion->value('iucn_status');                     // Vulnerable (VU)
$lion->value('family');                          // Felidae
$lion->identifiers()->keys();                    // gbif:4CGXP, gbif:5219404, ncbi.taxon:9689
$lion->related('parent')->keys();                // gbif:6DBT (Panthera)
$gbif->search(new Query('Panthera leo', limit: 10));

omnilab:
    sources:
        gbif:
            factory: gbif
            options:
                mailto: '[e-mail]'   # in the User-Agent, as GBIF asks: whom it writes to before it slows a caller down
                ncbi: true                     # read the NCBI id (one call more)
                language: 'eng'                # the common names a search result keeps (ISO 639-2)

With NCBI and Wikidata configured too, the Collector follows a species from one to the others: $collector->collect('gbif', 'Panthera leo') reaches NCBI Taxonomy by the NCBI id GBIF keeps for it, and Wikidata by its GBIF key (P14607) or, for an item that has none yet, its legacy number (P846).

Terms of use

GBIF's API is free and needs no key; GBIF asks a client to name itself in its User-Agent (a URL or an address: set mailto), publishes no fixed rate and answers 429 to a caller it slows down - its search APIs first, when its servers are loaded. The checklists are under the licences their publishers chose (the Catalogue of Life's is CC BY 4.0): cite GBIF and the Catalogue of Life where you show them.

See docs/ for what is read, how it maps, and what GBIF does not give here.

License: MIT.