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db-metabolomics-workbench

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

Updated Mar 13, 2026
Search Tags:#api#metabolomics#mass spectrometry#data retrieval#nih#workbench#refmet
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-metabolomics-workbench
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: db-metabolomics-workbench
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-metabolomics-workbench
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-metabolomics-workbench

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 users to query vast amounts of metabolomics data, standardize metabolite nomenclature, and retrieve experimental details for research and discovery.

Core Features & Use Cases

  • Query Metabolite Data: Access structures, identifiers, and cross-references for over 4,200 studies.
  • Standardize Nomenclature: Use RefMet to ensure consistent metabolite naming.
  • Search MS Data: Perform m/z searches to identify compounds.
  • Retrieve Study Information: Get metadata, experimental factors, and raw data from studies.
  • Use Case: A researcher needs to find all studies related to "diabetes" that measured "glucose" using LC-MS in human plasma. This Skill can retrieve that specific study data.

Quick Start

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

Frequently Asked Questions about db-metabolomics-workbench

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

FAQPage Schema
How do I retrieve metabolomics study metadata from the NIH Metabolomics Workbench?▼

You can retrieve metabolomics study metadata by querying the NIH Metabolomics Workbench REST API to fetch JSON or TXT data containing study details, experimental factors, and raw data for over 4,200 studies.

How do I standardize metabolite nomenclature for mass spectrometry data?▼

You standardize metabolite nomenclature by using the RefMet system provided through the NIH Metabolomics Workbench API to ensure consistent metabolite naming across studies and biomarker discovery workflows.

Can I search for metabolites by m/z values using the NIH Metabolomics Workbench API?▼

Yes, you can search for metabolites by querying specific m/z values through the NIH Metabolomics Workbench REST API to identify compounds and retrieve their structures and identifiers.

What data formats are available when querying metabolites from the Metabolomics Workbench?▼

When querying metabolites from the Metabolomics Workbench REST API, data is returned in JSON or TXT formats, allowing you to retrieve metabolite structures, identifiers, cross-references, and study metadata.

Does the NIH Metabolomics Workbench API require authentication to fetch study data?▼

The NIH Metabolomics Workbench API facilitates data retrieval for metabolites and studies without mentioning authentication requirements, requiring only API interaction to fetch JSON or TXT formatted data.

How do I find specific metabolomics studies filtered by disease and compound in human plasma?▼

You find specific metabolomics studies by querying the Metabolomics Workbench REST API with metabolite identifiers, study metadata, and experimental parameters to retrieve targeted research data.

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