metabolomics-workbench-database

Query the NIH Metabolomics Workbench REST API for metabolites and study data.

Updated Mar 10, 2026

Search Tags:#research #database #api #metabolomics #biomarker #nih

Ready to run

npx skills add https://github.com/felixboehm/biochem-allergy --skill metabolomics-workbench-database-felixboehm

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/metabolomics-workbench-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill metabolomics-workbench-database-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the NIH Metabolomics Workbench, a vast repository of metabolomics data, enabling researchers to query metabolites, studies, and associated biological information efficiently.

Core Features & Use Cases

Metabolite Discovery: Search for metabolites by name, mass, or chemical identifiers.
Study Data Access: Retrieve metadata and experimental data from thousands of metabolomics studies.
Nomenclature Standardization: Use RefMet to standardize metabolite names.
Mass Spectrometry Analysis: Perform m/z searches to identify compounds from experimental data.
Use Case: A researcher can use this skill to find all studies related to "diabetes" that measured "glucose" using LC-MS, and then download the raw data for further analysis.

Quick Start

Use the metabolomics-workbench-database skill to find all 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 query the NIH Metabolomics Workbench REST API for metabolite data?▼

Query the NIH Metabolomics Workbench REST API by searching for metabolites using chemical names, masses, or identifiers to retrieve structured metabolomics data and study metadata.

Can I identify a compound from an m/z value using the Metabolomics Workbench database?▼

Yes, you can perform m/z searches against the Metabolomics Workbench database to identify unknown compounds from mass spectrometry experimental data.

How do I standardize metabolite nomenclature across different studies?▼

Standardize metabolite nomenclature by applying the RefMet standardization system, which normalizes diverse metabolite names into a consistent format for cross-study analysis.

What is the best way to retrieve experimental results and study metadata for biomarker discovery?▼

Retrieve experimental results and study metadata by querying the Metabolomics Workbench REST API, which provides access to thousands of public metabolomics studies for biomarker discovery.

Can I search the Metabolomics Workbench database for metabolites related to a specific disease?▼

Yes, you can search the database for specific metabolites like glucose and filter associated studies by disease context such as diabetes to support targeted metabolomics research.

What are the limitations of using the Metabolomics Workbench API for compound identification?▼

The API relies on the Metabolomics Workbench repository, meaning compound identification is limited to the public data available within this specific NIH database and its RefMet nomenclature system.