Hmdb Tools

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

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

Available Tools

HMDB_get_diseases (Type: HMDBTool)

Get disease and pathway associations for a metabolite from HMDB. Returns diseases linked to abnor…

HMDB_get_diseases tool specification

Tool Information:

  • Name: HMDB_get_diseases

  • Type: HMDBTool

  • Description: Get disease and pathway associations for a metabolite from HMDB. Returns diseases linked to abnormal metabolite levels and metabolic pathways. Useful for biomarker discovery and metabolic disorder research.

Parameters:

  • operation (string) (required) No description

  • hmdb_id (string) (required) HMDB ID

Example Usage:

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

HMDB_get_metabolite (Type: HMDBTool)

Get human metabolite information from HMDB by ID. Returns name, formula, SMILES, classification, …

HMDB_get_metabolite tool specification

Tool Information:

  • Name: HMDB_get_metabolite

  • Type: HMDBTool

  • Description: Get human metabolite information from HMDB by ID. Returns name, formula, SMILES, classification, pathways, and disease associations. HMDB contains 220,000+ metabolites. No authentication required.

Parameters:

  • operation (string) (required) No description

  • hmdb_id (string) (required) HMDB ID (e.g., HMDB0000001 or 0000001)

Example Usage:

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

HMDB_search (Type: HMDBTool)

Search HMDB for metabolites by name, formula, or mass. Returns matching metabolites with HMDB IDs…

HMDB_search tool specification

Tool Information:

  • Name: HMDB_search

  • Type: HMDBTool

  • Description: Search HMDB for metabolites by name, formula, or mass. Returns matching metabolites with HMDB IDs and basic information. Essential for metabolite identification.

Parameters:

  • operation (string) (required) No description

  • query (string) (required) Search query - metabolite name, formula, or keyword

  • search_type (string) (optional) Search type: name, formula, mass (default: name)

Example Usage:

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