Metabolomics Workbench Tools

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

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

Available Tools

MetabolomicsWorkbench_get_compound_by_pubchem_cid (Type: MetabolomicsWorkbenchTool)

Get metabolite information by PubChem compound ID (CID). Useful for cross-referencing with PubChe…

MetabolomicsWorkbench_get_compound_by_pubchem_cid tool specification

Tool Information:

  • Name: MetabolomicsWorkbench_get_compound_by_pubchem_cid

  • Type: MetabolomicsWorkbenchTool

  • Description: Get metabolite information by PubChem compound ID (CID). Useful for cross-referencing with PubChem data.

Parameters:

  • input_value (string) (required) PubChem compound ID (CID) as a string (e.g., ‘311’ for citric acid).

  • output_item (string) (optional) Type of output to return.

Example Usage:

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

MetabolomicsWorkbench_get_refmet_info (Type: MetabolomicsWorkbenchTool)

Get RefMet standardized nomenclature for a metabolite. RefMet provides consistent, standardized m…

MetabolomicsWorkbench_get_refmet_info tool specification

Tool Information:

  • Name: MetabolomicsWorkbench_get_refmet_info

  • Type: MetabolomicsWorkbenchTool

  • Description: Get RefMet standardized nomenclature for a metabolite. RefMet provides consistent, standardized metabolite names across studies.

Parameters:

  • input_value (string) (required) Metabolite name to look up in RefMet (e.g., ‘Glucose’, ‘Palmitic acid’).

  • output_item (string) (optional) Type of information to return.

Example Usage:

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

MetabolomicsWorkbench_get_study (Type: MetabolomicsWorkbenchTool)

Get metadata and information about a metabolomics study by its study ID. Returns study summary in…

MetabolomicsWorkbench_get_study tool specification

Tool Information:

  • Name: MetabolomicsWorkbench_get_study

  • Type: MetabolomicsWorkbenchTool

  • Description: Get metadata and information about a metabolomics study by its study ID. Returns study summary including title, subject species, analysis type, and metabolites.

Parameters:

  • study_id (string) (required) Metabolomics Workbench study ID (e.g., ‘ST000001’, ‘ST000100’).

  • output_item (string) (optional) Type of information to return. Options: ‘summary’ (study overview), ‘factors’ (experimental factors), ‘analysis’ (analysis methods), ‘metabolites’ (metabolite list), ‘data’ (full data matrix).

Example Usage:

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

MetabolomicsWorkbench_search_by_exact_mass (Type: MetabolomicsWorkbenchTool)

Search metabolites by exact molecular mass. Useful for identifying unknown metabolites from high-…

MetabolomicsWorkbench_search_by_exact_mass tool specification

Tool Information:

  • Name: MetabolomicsWorkbench_search_by_exact_mass

  • Type: MetabolomicsWorkbenchTool

  • Description: Search metabolites by exact molecular mass. Useful for identifying unknown metabolites from high-resolution mass spectrometry.

Parameters:

  • mass_value (number) (required) The exact mass value to search for in Daltons (e.g., 180.0634).

  • tolerance (number) (optional) Mass tolerance in Daltons for the search.

Example Usage:

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

MetabolomicsWorkbench_search_by_mz (Type: MetabolomicsWorkbenchTool)

Search metabolites by m/z (mass-to-charge ratio) value from mass spectrometry data. Essential for…

MetabolomicsWorkbench_search_by_mz tool specification

Tool Information:

  • Name: MetabolomicsWorkbench_search_by_mz

  • Type: MetabolomicsWorkbenchTool

  • Description: Search metabolites by m/z (mass-to-charge ratio) value from mass spectrometry data. Essential for metabolite identification from MS experiments.

Parameters:

  • mz_value (number) (required) The m/z value to search for (e.g., 180.0634 for glucose [M+H]+).

  • adduct (string) (optional) Adduct type. Common values: ‘M+H’ (protonated), ‘M-H’ (deprotonated), ‘M+Na’ (sodiated), ‘M+K’ (potassiated).

  • tolerance (number) (optional) Mass tolerance in Daltons for the search.

Example Usage:

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

MetabolomicsWorkbench_search_compound_by_name (Type: MetabolomicsWorkbenchTool)

Search for a metabolite/compound by its name using RefMet nomenclature. Returns standardized comp…

MetabolomicsWorkbench_search_compound_by_name tool specification

Tool Information:

  • Name: MetabolomicsWorkbench_search_compound_by_name

  • Type: MetabolomicsWorkbenchTool

  • Description: Search for a metabolite/compound by its name using RefMet nomenclature. Returns standardized compound information including formula, exact mass, and classification. Use this for finding metabolites by common name.

Parameters:

  • input_value (string) (required) Compound/metabolite name to search (e.g., ‘Glucose’, ‘Cholesterol’, ‘Palmitic acid’).

  • output_item (string) (optional) Type of output to return.

Example Usage:

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