Can I search for metabolites by mass spectrometry values?

Yes, you can search by m/z (mass-to-charge ratio) values, specify ion adducts like M+H or M-H, and set a mass tolerance for matching.

How does this skill help with metabolite naming consistency?

It utilizes the RefMet database to map common or synonymous metabolite names to a standardized nomenclature and hierarchical chemical classification.

What data formats does the skill support?

The skill supports both JSON for machine-readable programmatic access and TXT for human-readable tab-delimited experimental data.

What is the primary data source for this skill?

This skill interacts with the NIH Common Fund-sponsored Metabolomics Workbench repository hosted at UCSD, providing access to thousands of public metabolomics studies.

Can I filter studies by specific diseases or tissues?

Yes, using the MetStat functionality, you can filter studies by parameters such as species (e.g., Human), sample source (e.g., Blood), and disease state (e.g., Diabetes).

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: Microck

byMicrock

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Data Science & ML

Accesses the NIH Metabolomics Workbench REST API to query metabolite structures, experimental studies, and mass spectrometry data.

This skill provides a comprehensive interface for Claude to interact with the NIH Common Fund-sponsored Metabolomics Workbench, the primary repository for metabolomics research data. It enables users to programmatically access over 4,200 processed studies, retrieve standardized metabolite nomenclature through RefMet, and perform complex searches across mass spectrometry (GC-MS, LC-MS) and NMR platforms. Whether you are performing biomarker discovery, standardizing chemical names for meta-analysis, or identifying compounds from m/z values, this skill streamlines the process of extracting high-quality metabolomics data for research and computational analysis.

Key Features

01Retrieve gene and protein associations linked to specific metabolites and metabolic pathways

02Query comprehensive study metadata and experimental results from over 4,200 NIH-sponsored studies

03Perform precursor ion mass searches (m/z) with specific ion adducts and mass tolerances

04Standardize metabolite nomenclature using the RefMet database across four structural resolution levels

0581 GitHub stars

06Filter studies by analytical method, ionization polarity, species, and specific disease states

Use Cases

01Identifying potential chemical compounds from mass spectrometry m/z values and ion adducts

02Normalizing metabolite datasets for meta-analysis using systematic RefMet classifications

03Aggregating experimental results across multiple studies for specific biomarkers or disease states

What are Skills?·How to Install

Install with 🐟 Skill.Fish

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

For use in Claude.ai and ChatGPT

Download Skill