Bacdive Tools#

Configuration File: bacdive_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

BacDive_get_strain (Type: BacDiveTool)#

Retrieve one BacDive strain’s curated phenotype: taxonomy down to species, cell morphology and Gr…

BacDive_get_strain tool specification

Tool Information:

  • Name: BacDive_get_strain

  • Type: BacDiveTool

  • Description: Retrieve one BacDive strain’s curated phenotype: taxonomy down to species, cell morphology and Gram stain, culture temperatures and media, oxygen tolerance, isolation source, and biosafety risk group. Complements GTDB (taxonomy only) and MGnify (metagenomes) by describing how the organism actually grows. Example: bacdive_id=24493. Use BacDive_search_by_taxon to find IDs.

Parameters:

  • bacdive_id ([‘integer’, ‘string’]) (required) BacDive strain ID, e.g. 24493.

Example Usage:

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

BacDive_search_by_taxon (Type: BacDiveTool)#

List BacDive strain IDs described for a bacterial or archaeal taxon. BacDive is the DSMZ strain-l…

BacDive_search_by_taxon tool specification

Tool Information:

  • Name: BacDive_search_by_taxon

  • Type: BacDiveTool

  • Description: List BacDive strain IDs described for a bacterial or archaeal taxon. BacDive is the DSMZ strain-level phenotype resource and a Global Core Biodata Resource, covering morphology, growth conditions, physiology, and isolation source for 100k+ strains. Give genus alone, or genus plus species. Example: genus=’Bacillus’, species=’subtilis’. Pass a returned bacdive_id to BacDive_get_strain for the full phenotype.

Parameters:

  • genus (string) (required) Genus name, capitalized, e.g. ‘Bacillus’.

  • species ([‘string’, ‘null’]) (optional) Species epithet, lowercase, e.g. ‘subtilis’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum strain IDs to return (default 25, max 100).

Example Usage:

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