Metabolite Tools#

Configuration File: metabolite_tools.json Tool Type: Local Tools Count: 6

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

Available Tools#

HMDB_get_diseases (Type: MetaboliteTool)#

Alias for Metabolite_get_diseases. Get CTD disease associations for a metabolite with recoverable…

HMDB_get_diseases tool specification

Tool Information:

  • Name: HMDB_get_diseases

  • Type: MetaboliteTool

  • Description: Alias for Metabolite_get_diseases. Get CTD disease associations for a metabolite with recoverable offset pagination. Provide an HMDB ID, compound name, or PubChem CID; continue with next_offset while has_more is true.

Parameters:

  • operation (string) (optional) No description

  • hmdb_id (string) (optional) HMDB ID (e.g., HMDB0000122)

  • compound_name (string) (optional) Compound name (e.g., glucose)

  • pubchem_cid (string) (optional) PubChem CID as an alternative identifier to hmdb_id or compound_name.

  • limit (integer) (optional) Maximum number of disease associations to return (default 50).

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

Example Usage:

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

HMDB_get_metabolite (Type: MetaboliteTool)#

Alias for Metabolite_get_info. Get compound information by HMDB ID, compound name, or PubChem CID.

HMDB_get_metabolite tool specification

Tool Information:

  • Name: HMDB_get_metabolite

  • Type: MetaboliteTool

  • Description: Alias for Metabolite_get_info. Get compound information by HMDB ID, compound name, or PubChem CID.

Parameters:

  • operation (string) (optional) No description

  • hmdb_id (string) (optional) HMDB ID (e.g., HMDB0000122)

  • compound_name (string) (optional) Compound name (e.g., glucose)

Example Usage:

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

HMDB_search (Type: MetaboliteTool)#

Alias for Metabolite_search. Search for metabolites by compound name or molecular formula via Pub…

HMDB_search tool specification

Tool Information:

  • Name: HMDB_search

  • Type: MetaboliteTool

  • Description: Alias for Metabolite_search. Search for metabolites by compound name or molecular formula via PubChem. Accepts common names, synonyms (e.g., ‘glucosylceramide’, ‘glucose’, ‘ATP’).

Parameters:

  • operation (string) (optional) No description

  • query (string) (required) Compound name or molecular formula to search

Example Usage:

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

Metabolite_get_diseases (Type: MetaboliteTool)#

Get curated disease associations for a metabolite using mydisease.info’s BioThings cache of CTD (…

Metabolite_get_diseases tool specification

Tool Information:

  • Name: Metabolite_get_diseases

  • Type: MetaboliteTool

  • Description: Get curated disease associations for a metabolite using mydisease.info’s BioThings cache of CTD (Comparative Toxicogenomics Database). Accepts HMDB ID, compound name, or PubChem CID. Resolves the identifier through PubChem, fetches every mydisease hit across server pages, and returns a resumable association page with disease ID, direct CTD evidence when present, and supporting PubMed IDs. data.disease_count and metadata.total_results report the full matched association count.

Parameters:

  • operation (string) (optional) No description

  • hmdb_id (string) (optional) HMDB ID (e.g., HMDB0000122)

  • compound_name (string) (optional) Compound name (e.g., glucose, cholesterol)

  • pubchem_cid ([‘integer’, ‘string’]) (optional) PubChem CID (e.g., 5793)

  • limit (integer) (optional) Page size for disease associations (default: 50)

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

Example Usage:

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

Metabolite_get_info (Type: MetaboliteTool)#

Get compound information for a metabolite by HMDB ID, compound name, or PubChem CID. Returns comm…

Metabolite_get_info tool specification

Tool Information:

  • Name: Metabolite_get_info

  • Type: MetaboliteTool

  • Description: Get compound information for a metabolite by HMDB ID, compound name, or PubChem CID. Returns common name, IUPAC name, molecular formula, molecular weight, canonical SMILES, and InChIKey via PubChem. Accepts HMDB IDs (e.g., HMDB0000122), compound names (e.g., glucose), or PubChem CIDs (numeric).

Parameters:

  • operation (string) (optional) No description

  • hmdb_id (string) (optional) HMDB ID (e.g., HMDB0000122 or HMDB0000001)

  • compound_name (string) (optional) Compound name (e.g., glucose, L-alanine, caffeine)

  • pubchem_cid ([‘integer’, ‘string’]) (optional) PubChem CID (e.g., 5793)

Example Usage:

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

Metabolite_search (Type: MetaboliteTool)#

Search for metabolites by compound name or molecular formula via PubChem. Returns a resumable res…

Metabolite_search tool specification

Tool Information:

  • Name: Metabolite_search

  • Type: MetaboliteTool

  • Description: Search for metabolites by compound name or molecular formula via PubChem. Returns a resumable result page with PubChem CID, name, formula, molecular weight, and SMILES. Use search_type=’name’ for name/keyword search (default) or search_type=’formula’ for exact molecular formula search (e.g., C6H12O6). metadata.total_results reports the full count for exact name/formula results; autocomplete fallbacks explicitly set metadata.result_set_complete=false because PubChem autocomplete exposes no authoritative total.

Parameters:

  • operation (string) (optional) No description

  • query (string) (required) Search query: compound name (e.g., glucose) or molecular formula (e.g., C6H12O6)

  • search_type (string) (optional) Search type: ‘name’ for compound name search, ‘formula’ for molecular formula search (default: name)

  • limit (integer) (optional) Page size (default 10, maximum 50).

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

Example Usage:

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