How does the RefMet feature work?

RefMet standardizes metabolite nomenclature, allowing you to match common names to a systematic classification across four structural resolution levels.

Does this require an API key?

The Metabolomics Workbench REST API is generally public and does not require a private API key for standard research queries.

Can I search for metabolites by mass?

Yes, the skill allows you to perform m/z searches across multiple databases with specific ion adducts (like M+H or M-H) and custom mass tolerances.

What is the Metabolomics Workbench?

It is an NIH-sponsored platform hosted at UCSD that serves as the primary repository for metabolomics research data, including thousands of public studies.

Is this skill suitable for human disease research?

Absolutely. It supports filtering studies by biological parameters, including species (like Human), sample sources, and specific diseases like Diabetes or Cancer.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: Microck

byMicrock

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Data Science & ML

Accesses the NIH Metabolomics Workbench to query metabolite data, study metadata, and standardized chemical nomenclature.

About

The Metabolomics Workbench Database skill provides programmatic access to the NIH Common Fund-sponsored repository of metabolomics research, containing over 4,200 studies. It enables researchers and developers to perform advanced mass spectrometry searches, retrieve experimental results, and utilize the RefMet database for standardized chemical nomenclature. Whether conducting biomarker discovery or retrieving experimental data across LC-MS, GC-MS, and NMR platforms, this skill streamlines the integration of large-scale metabolic datasets into Claude-driven research and analysis workflows.

Key Features

81 GitHub stars
Advanced mass spectrometry (m/z) searches with custom adducts
Support for structured JSON and tab-delimited text formats
Standardized metabolite nomenclature using the RefMet database
Cross-referencing for gene and protein-metabolite associations
Comprehensive study metadata and experimental data retrieval

Use Cases

Identifying unknown chemical compounds from raw mass spectrometry m/z values
Standardizing inconsistent metabolite names in large research datasets
Retrieving comparative experimental data for specific diseases or analytical platforms

About

Key Features

81 GitHub stars
Advanced mass spectrometry (m/z) searches with custom adducts
Support for structured JSON and tab-delimited text formats
Standardized metabolite nomenclature using the RefMet database
Cross-referencing for gene and protein-metabolite associations
Comprehensive study metadata and experimental data retrieval

Use Cases

Identifying unknown chemical compounds from raw mass spectrometry m/z values
Standardizing inconsistent metabolite names in large research datasets
Retrieving comparative experimental data for specific diseases or analytical platforms