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. Results are sorted by valid run count and expose total_matches, has_more, truncated, and next_offset metadata for complete retrieval.

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.

  • offset (integer) (optional) Zero-based result offset. Continue with metadata.next_offset while has_more is true.

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. Results are sorted by presented sample count and expose total_matches, has_more, truncated, and next_offset metadata for complete retrieval.

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.

  • offset (integer) (optional) Zero-based result offset. Continue with metadata.next_offset while has_more is true.

Example Usage:

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