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metabolomics-workbench-database

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

Updated Dec 17, 2025
Search Tags:#data analysis#bioinformatics#metabolomics#biomarker discovery#workbench
One-click install
npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill metabolomics-workbench-database-robotlearning123
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/metabolomics-workbench-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill metabolomics-workbench-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to the NIH Metabolomics Workbench database, offering comprehensive metabolomics research data and enabling users to query metabolites, RefMet nomenclature, MS/NMR data, and study metadata for metabolomics and biomarker discovery.

Core Features & Use Cases

  • Metabolite Querying: Access metabolite structures, identifiers, and cross-references to external databases.
  • Study Data Access: Retrieve study summaries, experimental factors, and analysis details.
  • Nomenclature Standardization: Use RefMet to standardize metabolite names and access systematic classification.
  • Mass Spectrometry Searches: Perform m/z searches and calculate exact masses for known metabolites.
  • Study Filtering: Filter studies by analytical and biological parameters using MetStat.
  • Gene and Protein Information: Retrieve gene and protein data associated with metabolic pathways.
  • Use Case: Imagine you need to identify potential biomarkers for a specific disease. Use this Skill to query metabolomics studies, perform m/z searches, and access gene-protein-metabolite associations.

Quick Start

Use the metabolomics-workbench-database skill to search for metabolite information using the name 'glucose'.

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 metabolomics study data from the NIH Metabolomics Workbench?▼

Query metabolomics study data by using the Skill to send requests to NIH Metabolomics Workbench REST API endpoints, retrieving study summaries, experimental factors, and analysis details. You can filter studies by analytical and biological parameters using MetStat to refine your biomarker discovery research.

Can I standardize metabolite nomenclature for mass spectrometry data using RefMet?▼

Standardize metabolite nomenclature using RefMet to access systematic classification and standardize metabolite names for mass spectrometry data. This allows you to perform m/z searches and calculate exact masses for known metabolites directly through the Metabolomics Workbench database.

What's the best way to search for metabolites by m/z value in metabolomics research?▼

Perform m/z searches and calculate exact masses for known metabolites by querying the Metabolomics Workbench database. You can retrieve metabolite structures, identifiers, and cross-references to external databases to support your biomarker discovery workflow.

Does this Skill require any specific dependencies to access metabolomics data?▼

Accessing metabolomics data requires the requests library to query REST API endpoints for various data types and contexts. The Skill relies on requests to interact with the NIH Metabolomics Workbench database for study retrieval, metabolite querying, and mass spectrometry searching.

How do I retrieve gene and protein information associated with metabolic pathways?▼

Retrieve gene and protein data associated with metabolic pathways by querying the Metabolomics Workbench database through REST API endpoints. This enables you to access gene-protein-metabolite associations, which is useful for identifying potential biomarkers for specific diseases.

What are the limitations of using Metabolomics Workbench for biomarker discovery?▼

Biomarker discovery using the Metabolomics Workbench is limited to the data available in the NIH database via REST API endpoints. You can filter studies by analytical and biological parameters using MetStat, but results depend on the coverage and metadata completeness of submitted metabolomics studies.

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