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metabolomics-workbench-database

Query the NIH Metabolomics Workbench REST API for metabolomics data.

Updated Mar 10, 2026
Search Tags:#database#metabolomics#biomarker discovery#mass spectrometry#nih#refmet
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill metabolomics-workbench-database-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill metabolomics-workbench-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the NIH Metabolomics Workbench, enabling researchers to query vast datasets of metabolomics studies, standardize metabolite names, and perform mass spectrometry searches, accelerating biomarker discovery and scientific research.

Core Features & Use Cases

  • Query Metabolite Data: Access structures, identifiers, and cross-references for thousands of metabolites.
  • Access Study Data: Retrieve metadata and experimental results from over 4,200 metabolomics studies.
  • Standardize Nomenclature: Use RefMet to ensure consistent metabolite naming.
  • Perform MS Searches: Identify compounds by m/z values with specified adducts and tolerances.
  • Use Case: A researcher needs to find all studies related to "glucose" metabolism in human blood samples using LC-MS. This Skill can query the Metabolomics Workbench to identify relevant studies and retrieve their associated data.

Quick Start

Use the metabolomics-workbench-database skill to find studies containing the metabolite 'Tyrosine'.

Frequently Asked Questions about metabolomics-workbench-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I access NIH Metabolomics Workbench data programmatically?▼

You can access NIH Metabolomics Workbench data programmatically by querying the REST API to retrieve metabolite structures, study metadata, experimental results, and standardized RefMet nomenclature.

Can I search for metabolites using mass spectrometry m/z values?▼

Yes, you can perform mass spectrometry searches by specifying m/z values, adducts, and tolerances to identify compounds within the NIH Metabolomics Workbench database.

What is RefMet nomenclature and how is it used in metabolomics research?▼

RefMet is a standardized nomenclature system used in metabolomics to ensure consistent metabolite naming across studies, enabling accurate cross-referencing of metabolite structures and identifiers.

How do I find metabolomics studies filtered by biological parameters like human blood samples?▼

You can filter metabolomics studies by biological and analytical parameters such as species, specimen, or LC-MS method to identify relevant studies and retrieve their associated experimental results.

Do I need Python to retrieve metabolomics data from the Metabolomics Workbench?▼

Python is used for programmatic data retrieval and analysis by integrating with the requests library to query the REST API, allowing you to automate fetching metabolite structures and study data.

What limitations exist when querying metabolite structures through the Metabolomics Workbench API?▼

Limitations include dependency on REST API availability and rate limits, and the need for exact m/z tolerances and accurate RefMet names to retrieve precise metabolite structures and study metadata.

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