Gbif Ext Tools

Configuration File: gbif_ext_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the gbif_ext_tools.json configuration file.

Available Tools

GBIF_get_species (Type: BaseRESTTool)

Get detailed species information from the Global Biodiversity Information Facility (GBIF) by its …

GBIF_get_species tool specification

Tool Information:

  • Name: GBIF_get_species

  • Type: BaseRESTTool

  • Description: Get detailed species information from the Global Biodiversity Information Facility (GBIF) by its taxon key. Returns the full taxonomic record including scientific name, authorship, rank, full classification (kingdom through species), taxonomic status, basionym, vernacular name, and number of descendant taxa. Use GBIF_search_species first to find taxon keys. Example: key 2435099 returns Puma concolor (puma) with full classification from Animalia to Puma concolor.

Parameters:

  • speciesKey (integer) (required) GBIF species/taxon key. Examples: 2435099 (Puma concolor / puma), 2878688 (Quercus robur / English oak), 5219404 (Canis lupus / wolf), 2480528 (Homo sapiens), 2495662 (Aquila chrysaetos / golden eagle). Use GBIF_search_species to find keys.

Example Usage:

query = {
    "name": "GBIF_get_species",
    "arguments": {
        "speciesKey": 10
    }
}
result = tu.run(query)

GBIF_match_name (Type: BaseRESTTool)

Resolve a free-text scientific name to the single best-matching GBIF Backbone taxon. Unlike GBIF_…

GBIF_match_name tool specification

Tool Information:

  • Name: GBIF_match_name

  • Type: BaseRESTTool

  • Description: Resolve a free-text scientific name to the single best-matching GBIF Backbone taxon. Unlike GBIF_search_species / GBIF_suggest_species (which return ranked candidate lists), this returns the one authoritative match with a stable usageKey (taxonKey), matchType (EXACT/FUZZY/HIGHERRANK/NONE), a confidence score (0-100), taxonomic status, and the full key-bearing lineage (kingdomKey..speciesKey). This is the GBIF-recommended way to map names to stable taxon keys for downstream occurrence queries. Example: name=’Puma concolor’ -> usageKey 2435099, matchType EXACT, confidence 99. No API key required.

Parameters:

  • name (string) (required) Scientific name to match, e.g. ‘Puma concolor’, ‘Quercus robur’, ‘Homo sapiens’.

  • kingdom ([‘string’, ‘null’]) (optional) Optional kingdom to disambiguate homonyms, e.g. ‘Animalia’, ‘Plantae’.

  • rank ([‘string’, ‘null’]) (optional) Optional rank hint, e.g. ‘SPECIES’, ‘GENUS’.

  • strict ([‘boolean’, ‘null’]) (optional) If true, only return exact matches (no fuzzy matching).

  • verbose ([‘boolean’, ‘null’]) (optional) If true, include alternative matches in the response.

Example Usage:

query = {
    "name": "GBIF_match_name",
    "arguments": {
        "name": "example_value"
    }
}
result = tu.run(query)

GBIF_occurrence_stats (Type: BaseRESTTool)

Get GBIF occurrence statistics for a taxonKey: the total occurrence count plus faceted breakdowns…

GBIF_occurrence_stats tool specification

Tool Information:

  • Name: GBIF_occurrence_stats

  • Type: BaseRESTTool

  • Description: Get GBIF occurrence statistics for a taxonKey: the total occurrence count plus faceted breakdowns (occurrences per country, year, basisOfRecord, or institutionCode). Unlike GBIF_search_occurrences (which returns raw records with no aggregation), this uses limit=0 with a facet parameter so it returns quantitative summaries over the whole matching set. Get a taxonKey from GBIF_match_name or GBIF_search_species. Example: taxonKey=2435099 (Puma concolor), facet=country -> count 29340 with per-country counts (US 11380, AR 3368, …). No API key required.

Parameters:

  • taxonKey (integer) (required) GBIF taxon key, e.g. 2435099 (Puma concolor). Obtain from GBIF_match_name or GBIF_search_species.

  • facet ([‘string’, ‘null’]) (optional) Field to break occurrence counts down by, e.g. ‘country’, ‘year’, ‘basisOfRecord’, or ‘institutionCode’. Default ‘country’.

  • facetLimit ([‘integer’, ‘null’]) (optional) Number of top facet values to return (default 10).

  • country ([‘string’, ‘null’]) (optional) Optional ISO 3166-1 alpha-2 country code filter, e.g. ‘US’.

Example Usage:

query = {
    "name": "GBIF_occurrence_stats",
    "arguments": {
        "taxonKey": 10
    }
}
result = tu.run(query)

GBIF_suggest_species (Type: BaseRESTTool)

Autocomplete species names using the GBIF species suggestion endpoint. Returns quick matches as y…

GBIF_suggest_species tool specification

Tool Information:

  • Name: GBIF_suggest_species

  • Type: BaseRESTTool

  • Description: Autocomplete species names using the GBIF species suggestion endpoint. Returns quick matches as you type, with basic taxonomic info (key, name, rank, classification). Faster and lighter than full search – designed for type-ahead interfaces and quick name resolution. Returns up to 20 suggestions. Example: ‘Quer’ matches Quercus (oaks), Quercus robur (English oak), etc.

Parameters:

  • q (string) (required) Partial or full species/taxon name to autocomplete. Examples: ‘Homo sap’, ‘Quercus’, ‘Pan trog’, ‘Escherichia’, ‘Drosoph’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum number of suggestions to return (1-20, default 10).

Example Usage:

query = {
    "name": "GBIF_suggest_species",
    "arguments": {
        "q": "example_value"
    }
}
result = tu.run(query)