What is the Metabolomics Workbench Skill?

It's a specialized capability for Claude Code that allows users to interact with the NIH Metabolomics Workbench REST API to find metabolite data, research studies, and chemical structures.

Can I find gene-metabolite associations?

Yes, the skill includes endpoints to query gene and protein information, including UniProt IDs and sequences, related to specific metabolic pathways.

What is RefMet and why is it used here?

RefMet is a standardized nomenclature system for metabolites; this skill uses it to ensure metabolite names are consistent across different studies and external databases like PubChem or KEGG.

Can I search for metabolites by mass?

Yes, the skill supports searching by mass-to-charge ratio (m/z) with specific ion adducts (like M+H or M-H) and customizable mass tolerances.

Does this skill support experimental data retrieval?

Yes, you can retrieve complete experimental results, factor details, and study summaries in both JSON and tab-delimited text formats.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: Activer007

byActiver007

0•

Data Science & ML

Accesses the NIH Metabolomics Workbench REST API to query metabolite data, standardized nomenclature, and experimental research studies.

This skill provides programmatic access to the NIH Common Fund's Metabolomics Workbench, a primary repository for metabolomics research data hosted at UCSD. It enables users to query over 4,200 processed studies, search for compounds by mass spectrometry (m/z) values, and standardize metabolite nomenclature using the RefMet database. Whether performing biomarker discovery, cross-referencing metabolite identifiers like PubChem or KEGG, or retrieving complete experimental datasets for analysis, this skill integrates comprehensive metabolic knowledge and analytical results directly into the AI development workflow.

Key Features

01Mass spectrometry (m/z) and adduct search capabilities

020 GitHub stars

03Retrieval of molecular structures and compound metadata

04Gene and protein association querying for metabolic pathways

05REST API access to 4,200+ metabolomics studies

06Metabolite name standardization via RefMet nomenclature

Use Cases

01Retrieving complete experimental datasets from public metabolomics studies

02Standardizing metabolite nomenclature for research data analysis

03Identifying unknown compounds from mass spectrometry (m/z) data

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