Does it support nomenclature standardization?

Yes, it utilizes the RefMet database to match common metabolite names to standardized, systematic nomenclature and hierarchical classifications.

What is the Metabolomics Workbench skill?

It is a specialized capability for Claude to programmatically access the NIH Metabolomics Workbench repository, the primary US repository for metabolomics research data.

Can it help identify metabolites from MS data?

Yes, the skill includes tools for mass-to-charge (m/z) searches across Metabolomics Workbench, LIPIDS, and RefMet databases with customizable tolerances and adduct types.

What data formats are supported by the API?

The API returns data in JSON for programmatic processing or TXT for human-readable tab-delimited formats.

How many studies can I access with this skill?

You can access metadata and experimental results from over 4,200 processed studies, with over 3,790 of them being publicly available.

Metabolomics Workbench Integration

Name: Metabolomics Workbench Integration
Author: Activer007

byActiver007

Data Science & ML

Accesses the NIH Metabolomics Workbench database to query metabolite structures, experimental study data, and standardized nomenclature.

About

This skill enables Claude to interact directly with the NIH Common Fund-sponsored Metabolomics Workbench API, providing access to over 4,200 processed studies. It facilitates searching for metabolites by various identifiers (PubChem CID, KEGG ID), standardizing chemical nomenclature via RefMet, and performing complex mass spectrometry m/z searches. It is an essential tool for researchers and bioinformaticians performing biomarker discovery, metabolic pathway analysis, or cross-referencing gene-metabolite associations within a standardized experimental framework across multiple analytical platforms like GC-MS, LC-MS, and NMR.

Key Features

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Retrieve complete experimental datasets and study metadata from 4,200+ studies
Query gene and protein associations related to metabolic pathways
Standardize metabolite names using the RefMet database nomenclature
Perform m/z searches with specific ion adducts and mass tolerances
Access metabolite structures, identifiers, and cross-references to external databases

Use Cases

Standardizing large lists of metabolite names for comparative meta-analysis
Identifying unknown compounds from mass spectrometry (m/z) data
Conducting disease-specific data mining across thousands of NIH metabolomics studies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Download Skill

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