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Zehong-Wang
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metabolomics-workbench-database

Query metabolite structures and study metadata via the NIH Metabolomics Workbench REST API.

Updated Aug 23, 2026
Search Tags:#data access#metabolomics#biomarker discovery#mass spectrometry#nih#refmet
One-click install
npx skills add https://github.com/Zehong-Wang/Kosmos --skill metabolomics-workbench-database-zehong-wang
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/Zehong-Wang/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/Zehong-Wang/Kosmos --skill metabolomics-workbench-database-zehong-wang

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 amounts of metabolomics data, standardize metabolite names, and retrieve study information efficiently.

Core Features & Use Cases

  • Metabolite Querying: Search for metabolites by name, formula, or mass, and retrieve their structures and identifiers.
  • Study Access: Find and download data from over 4,200 metabolomics studies.
  • Nomenclature Standardization: Use RefMet to ensure consistent metabolite naming.
  • Mass Spectrometry Search: Identify compounds based on m/z values.
  • Use Case: A researcher needs to find all studies related to "glucose" metabolism in human blood under "diabetes" conditions, using LC-MS. This Skill can retrieve that specific subset of studies and 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 search for metabolomics studies by metabolite name and disease condition?▼

Search metabolomics studies by querying the NIH Metabolomics Workbench REST API with specific metabolite names and disease conditions to retrieve targeted experimental results and study metadata.

How do I standardize metabolite nomenclature for biomarker discovery?▼

Standardize metabolite nomenclature using RefMet to ensure consistent metabolite naming across datasets, facilitating accurate biomarker discovery and cross-study comparisons.

Can I identify compounds using mass spectrometry m/z values?▼

Identify compounds by performing mass spectrometry searches with m/z values against the Metabolomics Workbench database to retrieve matching metabolite structures and identifiers.

How do I access metabolite structures and identifiers programmatically?▼

Access metabolite structures and identifiers programmatically by integrating Python requests with the Metabolomics Workbench REST API to query over 4,200 studies.

What is the best way to retrieve experimental results from NIH metabolomics studies?▼

Retrieve experimental results by querying the NIH Metabolomics Workbench REST API to access study metadata, metabolite structures, and experimental data across thousands of metabolomics studies.

Does this Skill support querying metabolites by chemical formula?▼

Yes, query metabolites by chemical formula through the Metabolomics Workbench REST API to retrieve corresponding metabolite structures, identifiers, and associated study data.

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