Gmrepo Tools

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

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

Available Tools

GMrepo_get_phenotypes (Type: GmrepoTool)

List phenotypes and health conditions with gut microbiome data in the GMrepo database. Returns Me…

GMrepo_get_phenotypes tool specification

Tool Information:

  • Name: GMrepo_get_phenotypes

  • Type: GmrepoTool

  • Description: List phenotypes and health conditions with gut microbiome data in the GMrepo database. Returns MeSH disease IDs, sample counts, and species/genus diversity for each phenotype. Optionally filter by keyword (e.g., ‘diabetes’, ‘obesity’, ‘cancer’). GMrepo covers 350+ phenotypes including healthy controls. Use this to find what conditions have microbiome data available.

Parameters:

  • query (string) (optional) Optional keyword to filter phenotypes. Examples: ‘diabetes’, ‘obesity’, ‘cancer’, ‘Healthy’, ‘Crohn’. Leave empty to list all phenotypes.

  • limit (integer) (optional) Maximum number of results to return. Default: 20.

Example Usage:

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

GMrepo_search_species (Type: GmrepoTool)

Search the GMrepo database for gut microbiome species by name. Returns species with NCBI taxon ID…

GMrepo_search_species tool specification

Tool Information:

  • Name: GMrepo_search_species

  • Type: GmrepoTool

  • Description: Search the GMrepo database for gut microbiome species by name. Returns species with NCBI taxon IDs, sample counts, prevalence across conditions, and number of associated phenotypes. GMrepo is a curated human gut microbiome repository with data from 96,000+ samples across 350+ phenotypes. Use this to find specific bacteria and their prevalence in human gut studies.

Parameters:

  • query (string) (required) Species name or partial name to search. Examples: ‘Akkermansia’, ‘Bacteroides’, ‘Lactobacillus’, ‘Faecalibacterium prausnitzii’, ‘Bifidobacterium’.

  • limit (integer) (optional) Maximum number of results to return. Default: 20.

Example Usage:

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