Metabolights Tools

Configuration File: metabolights_tools.json Tool Type: Local Tools Count: 9

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

Available Tools

metabolights_get_study (Type: MetaboLightsRESTTool)

Get detailed information about a specific MetaboLights study by study ID. Returns complete study …

metabolights_get_study tool specification

Tool Information:

  • Name: metabolights_get_study

  • Type: MetaboLightsRESTTool

  • Description: Get detailed information about a specific MetaboLights study by study ID. Returns complete study metadata including title, description, authors, and publication information.

Parameters:

  • study_id (string) (required) MetaboLights study ID (e.g., ‘MTBLS1’)

Example Usage:

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

metabolights_get_study_assays (Type: MetaboLightsRESTTool)

Get all assays associated with a MetaboLights study. Returns assay metadata including assay types…

metabolights_get_study_assays tool specification

Tool Information:

  • Name: metabolights_get_study_assays

  • Type: MetaboLightsRESTTool

  • Description: Get all assays associated with a MetaboLights study. Returns assay metadata including assay types, protocols, and measurement details.

Parameters:

  • study_id (string) (required) MetaboLights study ID

Example Usage:

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

metabolights_get_study_data_files (Type: MetaboLightsRESTTool)

Get data file listings for a MetaboLights study. Returns metadata about analytical data files (ra…

metabolights_get_study_data_files tool specification

Tool Information:

  • Name: metabolights_get_study_data_files

  • Type: MetaboLightsRESTTool

  • Description: Get data file listings for a MetaboLights study. Returns metadata about analytical data files (raw or processed spectra, peak lists, etc.) available for the study. This endpoint focuses specifically on data files and may differ from the generic files endpoint. Use this to discover which data files are available for download and analysis.

Parameters:

  • study_id (string) (required) MetaboLights study ID (e.g., ‘MTBLS1’). Use metabolights_list_studies or metabolights_search_studies to discover study IDs.

Example Usage:

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

metabolights_get_study_factors (Type: MetaboLightsRESTTool)

Get experimental factors (variables) for a MetaboLights study. Returns factor definitions such as…

metabolights_get_study_factors tool specification

Tool Information:

  • Name: metabolights_get_study_factors

  • Type: MetaboLightsRESTTool

  • Description: Get experimental factors (variables) for a MetaboLights study. Returns factor definitions such as treatment groups, time points, disease states, or other experimental variables. Each factor includes name, type, and controlled vocabulary annotations. Use this to understand what variables were studied and how samples were grouped.

Parameters:

  • study_id (string) (required) MetaboLights study ID (e.g., ‘MTBLS1’). Use metabolights_list_studies or metabolights_search_studies to discover study IDs.

Example Usage:

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

metabolights_get_study_files (Type: MetaboLightsRESTTool)

Get list of files associated with a MetaboLights study. Returns file metadata including file name…

metabolights_get_study_files tool specification

Tool Information:

  • Name: metabolights_get_study_files

  • Type: MetaboLightsRESTTool

  • Description: Get list of files associated with a MetaboLights study. Returns file metadata including file names, types, and download links. Note: The files endpoint frequently returns 500 errors (known MetaboLights API issue). This tool automatically falls back to extracting file information from the study endpoint, including FTP/HTTP URLs. If both methods fail, access files via MetaboLights website: https://www.ebi.ac.uk/metabolights/studies/{study_id}.

Parameters:

  • study_id (string) (required) MetaboLights study ID

Example Usage:

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

metabolights_get_study_protocols (Type: MetaboLightsRESTTool)

Get experimental protocols used in a MetaboLights study. Returns detailed protocol information in…

metabolights_get_study_protocols tool specification

Tool Information:

  • Name: metabolights_get_study_protocols

  • Type: MetaboLightsRESTTool

  • Description: Get experimental protocols used in a MetaboLights study. Returns detailed protocol information including sample collection, extraction, chromatography, and data acquisition methods. Each protocol includes name, type, description, and controlled vocabulary annotations. Use this to understand the experimental methodology used in the study.

Parameters:

  • study_id (string) (required) MetaboLights study ID (e.g., ‘MTBLS1’). Use metabolights_list_studies or metabolights_search_studies to discover study IDs.

Example Usage:

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

metabolights_get_study_samples (Type: MetaboLightsRESTTool)

Get all samples associated with a MetaboLights study. Returns sample metadata including sample na…

metabolights_get_study_samples tool specification

Tool Information:

  • Name: metabolights_get_study_samples

  • Type: MetaboLightsRESTTool

  • Description: Get all samples associated with a MetaboLights study. Returns sample metadata including sample names, characteristics, and factor values. Note: The samples endpoint may return 400 errors for some studies. This tool automatically falls back to extracting sample information from the study endpoint (ISA investigation structure). If both methods fail, access samples via MetaboLights website.

Parameters:

  • study_id (string) (required) MetaboLights study ID

Example Usage:

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

metabolights_list_studies (Type: MetaboLightsRESTTool)

List all MetaboLights studies with pagination. Returns a list of study IDs (e.g., ‘MTBLS1’, ‘MTBL…

metabolights_list_studies tool specification

Tool Information:

  • Name: metabolights_list_studies

  • Type: MetaboLightsRESTTool

  • Description: List all MetaboLights studies with pagination. Returns a list of study IDs (e.g., ‘MTBLS1’, ‘MTBLS2’). Use metabolights_get_study to get detailed information for a specific study ID.

Parameters:

  • size (integer) (optional) Number of studies per page (default: 20)

  • page (integer) (optional) Page number (default: 0)

Example Usage:

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

metabolights_search_studies (Type: MetaboLightsRESTTool)

Search MetaboLights studies by query string. Returns a list of matching study IDs. Use metaboligh…

metabolights_search_studies tool specification

Tool Information:

  • Name: metabolights_search_studies

  • Type: MetaboLightsRESTTool

  • Description: Search MetaboLights studies by query string. Returns a list of matching study IDs. Use metabolights_get_study with a study ID to get detailed metadata including titles, descriptions, and organism information.

Parameters:

  • query (string) (required) Search query string (e.g., organism name, disease, metabolite name)

  • size (integer) (optional) Number of results per page (default: 20)

  • page (integer) (optional) Page number (default: 0)

Example Usage:

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