Bold Systems Tools#

Configuration File: bold_systems_tools.json Tool Type: Local Tools Count: 3

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

Available Tools#

BOLDSystems_get_record (Type: BOLDSystemsTool)#

Retrieve a single BOLD (Barcode of Life Data System) DNA barcode record by its BOLD process ID. R…

BOLDSystems_get_record tool specification

Tool Information:

  • Name: BOLDSystems_get_record

  • Type: BOLDSystemsTool

  • Description: Retrieve a single BOLD (Barcode of Life Data System) DNA barcode record by its BOLD process ID. Returns full taxonomy, BIN cluster, collection metadata, and COI-5P INSDC accession. Example: process_id=’ABRMM002-06’ returns a Panthera leo record collected at the Metro Toronto Zoo.

Parameters:

  • process_id (string) (required) BOLD process ID, e.g. ‘ABRMM002-06’.

Example Usage:

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

BOLDSystems_search_by_bin (Type: BOLDSystemsTool)#

Search BOLD (Barcode of Life Data System) for all DNA barcode records sharing a BIN (Barcode Inde…

BOLDSystems_search_by_bin tool specification

Tool Information:

  • Name: BOLDSystems_search_by_bin

  • Type: BOLDSystemsTool

  • Description: Search BOLD (Barcode of Life Data System) for all DNA barcode records sharing a BIN (Barcode Index Number) – BOLD’s algorithmic, sequence-similarity-based species-cluster identifier, which often resolves identity where taxonomy alone cannot. Example: bin_id=’BOLD:AAD6819’ returns 51 specimen records of Panthera leo sharing that barcode cluster. This is a capability unique to BOLD; ToolUniverse’s iDigBio tools have no genetic barcode or BIN data.

Parameters:

  • bin_id (string) (required) BOLD BIN identifier, e.g. ‘BOLD:AAD6819’ (the ‘BOLD:’ prefix is added automatically if omitted).

  • limit ([‘integer’, ‘null’]) (optional) Max records to return, 1-200. Default 30.

Example Usage:

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

BOLDSystems_search_by_taxon (Type: BOLDSystemsTool)#

Search BOLD (Barcode of Life Data System) DNA barcode records by taxon. rank=’genus’/’family’/’or…

BOLDSystems_search_by_taxon tool specification

Tool Information:

  • Name: BOLDSystems_search_by_taxon

  • Type: BOLDSystemsTool

  • Description: Search BOLD (Barcode of Life Data System) DNA barcode records by taxon. rank=’genus’/’family’/’order’ filters server-side; rank=’species’ (e.g. ‘Panthera leo’) queries at genus level and filters client-side, since BOLD does not support server-side species filtering. Optionally narrow by country. Example: taxon_name=’Panthera’, rank=’genus’ returns all big-cat barcode records with BIN cluster IDs, COI-5P accession numbers, and collection metadata.

Parameters:

  • taxon_name (string) (required) Taxon name matching rank, e.g. ‘Panthera’ (genus), ‘Felidae’ (family), ‘Carnivora’ (order), or ‘Panthera leo’ (species).

  • rank ([‘string’, ‘null’]) (optional) Taxonomic rank of taxon_name. Default ‘genus’.

  • country ([‘string’, ‘null’]) (optional) Optional country/ocean name to narrow results, e.g. ‘Canada’.

  • limit ([‘integer’, ‘null’]) (optional) Max records to return, 1-200. Default 30.

Example Usage:

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