What is the Metabolomics Workbench?

The Metabolomics Workbench is an NIH-sponsored repository at UCSD that hosts data from thousands of metabolomics studies, providing standardized nomenclature and analytical results.

Can I access gene and protein data with this skill?

Yes, it includes endpoints to query genes by symbol and proteins by UniProt ID to explore their associations with metabolic pathways.

Why is RefMet standardization important?

RefMet provides a systematic naming convention and hierarchical classification, ensuring that metabolite data from different studies can be compared accurately.

How does this skill assist with metabolite identification?

It allows for m/z searches with specific ion adducts (like M+H or M-H) and adjustable mass tolerances to find matching metabolites across various databases.

Metabolomics Workbench Explorer

Name: Metabolomics Workbench Explorer
Author: Activer007

byActiver007

0•

Data Science & ML

Accesses the NIH Metabolomics Workbench API to retrieve experimental study data, metabolite structures, and standardized biochemical nomenclature.

The Metabolomics Workbench Explorer skill provides programmatic access to the NIH Common Fund's primary repository for metabolomics research. It enables researchers and developers to query over 4,200 processed studies, perform advanced mass spectrometry searches by m/z values, and standardize chemical names using the RefMet database. By integrating these capabilities directly into Claude, users can streamline biomarker discovery, map gene-metabolite associations, and extract high-fidelity experimental data from MS and NMR platforms for advanced bioinformatics analysis.

Key Features

01Standardized metabolite nomenclature via RefMet database integration

02Mass spectrometry m/z searching with ion adduct and tolerance support

03Molecular structure downloads in MOL and PNG formats

04Gene-protein-metabolite association mapping for pathway analysis

050 GitHub stars

06Comprehensive study metadata and experimental result retrieval

Use Cases

01Standardizing chemical datasets for meta-analysis using systematic RefMet classifications

02Identifying compounds from raw mass spectrometry data using precise m/z matching

03Retrieving large-scale experimental data from NIH studies for machine learning models

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