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)

Attempts to get disease associations for a metabolite from HMDB. Note: HMDB does not provide an o…

HMDB_get_diseases tool specification

Tool Information:

  • Name: HMDB_get_diseases

  • Type: HMDBTool

  • Description: Attempts to get disease associations for a metabolite from HMDB. Note: HMDB does not provide an open API for disease data. This tool always returns an error directing users to the HMDB website. For disease-metabolite relationships, consider using CTD or DisGeNET databases instead.

Parameters:

  • operation (string) (optional) No description

  • hmdb_id (string) (required) HMDB ID

Example Usage:

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

HMDB_get_metabolite (Type: HMDBTool)

Get human metabolite information from HMDB by ID. Returns basic chemical properties via PubChem c…

HMDB_get_metabolite tool specification

Tool Information:

  • Name: HMDB_get_metabolite

  • Type: HMDBTool

  • Description: Get human metabolite information from HMDB by ID. Returns basic chemical properties via PubChem cross-reference: IUPAC name, molecular formula, SMILES, InChIKey, and molecular weight. Note: HMDB has no open API; data is retrieved from PubChem using the HMDB ID as a cross-reference. Classification, pathways, and disease associations are not available programmatically.

Parameters:

  • operation (string) (optional) No description

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

Example Usage:

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

HMDB_search (Type: HMDBTool)

Search for metabolites by name or formula using PubChem. Returns PubChem CIDs (not HMDB IDs) with…

HMDB_search tool specification

Tool Information:

  • Name: HMDB_search

  • Type: HMDBTool

  • Description: Search for metabolites by name or formula using PubChem. Returns PubChem CIDs (not HMDB IDs) with name, formula, SMILES, and molecular weight. search_type=’name’ uses PubChem compound/name endpoint; search_type=’formula’ uses PubChem fastformula endpoint; search_type=’mass’ falls back to name search (mass-based search not supported). HMDB IDs are not included in results.

Parameters:

  • operation (string) (optional) 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": {
        "query": "example_value"
    }
}
result = tu.run(query)