metabolomics-workbench-database

Query metabolites, studies, and biological data via the NIH Metabolomics Workbench REST API.

Updated Mar 15, 2026

Search Tags:#database #metabolomics #biomarker discovery #mass spectrometry #nih #refmet

Ready to run

npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill metabolomics-workbench-database-sagunkayastha

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: metabolomics-workbench-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/metabolomics-workbench-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill metabolomics-workbench-database-sagunkayastha

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 research data, enabling efficient querying of metabolites, studies, and related biological information.

Core Features & Use Cases

Metabolite Data Access: Retrieve structures, identifiers, and cross-references for over 4,200 studies.
Study Information Retrieval: Search and access study metadata, experimental results, and untargeted data.
Nomenclature Standardization: Use RefMet to standardize metabolite names and classifications.
Mass Spectrometry Search: Query compounds by m/z values with specified adducts and tolerances.
Gene and Protein Data: Access associated gene and protein information.
Use Case: A researcher needs to find all studies related to "diabetes" that used "LCMS" with "positive" polarity and then identify specific metabolites measured in those studies.

Quick Start

Use the metabolomics-workbench-database skill to find all public studies containing the metabolite '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 metabolites and biological data from the NIH Metabolomics Workbench?▼

You can query the NIH Metabolomics Workbench by using this skill to access metabolites, studies, and biological data via the REST API using Python requests. It retrieves structures, study metadata, and gene or protein information directly from the database.

How do I standardize metabolite names for mass spectrometry research?▼

To standardize metabolite names for mass spectrometry research, you can use the RefMet nomenclature system provided by the NIH Metabolomics Workbench. This skill facilitates RefMet standardization to unify metabolite names and classifications across different studies.

Can I search for compounds using m/z values in the Metabolomics Workbench database?▼

Yes, you can search for compounds in the Metabolomics Workbench database using m/z values. This skill supports mass spectrometry searches by querying compounds based on specified m/z values, adducts, and tolerances via the REST API.

How do I find public studies related to a specific metabolite like glucose?▼

You can find public studies related to a specific metabolite like glucose by querying the NIH Metabolomics Workbench. This skill retrieves study metadata and experimental results for over 4,200 studies containing the specified metabolite.

What type of gene and protein information can I access from the metabolomics database?▼

The metabolomics database provides access to associated gene and protein information linked to specific metabolites and studies. You can retrieve this biological data alongside metabolite structures and cross-references through the REST API.

Does the Metabolomics Workbench REST API support filtering studies by experimental conditions like LCMS polarity?▼

Yes, the Metabolomics Workbench REST API supports searching study metadata by experimental conditions. You can filter studies based on specific parameters like LCMS and positive polarity, then identify the specific metabolites measured in those filtered results.