What is the Metabolomics Workbench?

The Metabolomics Workbench is an NIH-sponsored platform hosted at UCSD that serves as the primary repository for metabolomics research data, providing access to over 4,200 processed studies.

Does this skill support different analytical methods?

Yes, it can filter studies and data based on analytical platforms including LC-MS, GC-MS, and NMR, as well as chromatography types like HILIC and RP.

Can I retrieve gene and protein data with this skill?

Yes, the skill can query gene and protein information associated with specific metabolic pathways, including cross-references to RefSeq and UniProt IDs.

What is RefMet nomenclature?

RefMet is a standardized naming convention for metabolites. This skill uses it to resolve naming ambiguities and ensure consistent classification across different scientific datasets.

How does this skill assist with mass spectrometry?

It allows you to perform m/z (mass-to-charge ratio) searches with specified ion adducts and tolerance levels to identify potential metabolites directly within your AI workflow.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: ricable

byricable

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Data Science & ML

Integrates with the NIH Metabolomics Workbench REST API to query metabolite data, standardized nomenclature, and experimental studies for biomarker discovery.

This skill provides programmatic access to the NIH Common Fund-sponsored Metabolomics Workbench, the primary repository for metabolomics research. It allows users to query over 4,200 processed studies, access standardized metabolite nomenclature through RefMet, and perform mass spectrometry searches using m/z values. Whether performing biomarker discovery, standardizing chemical names, or retrieving experimental datasets from GC-MS, LC-MS, and NMR platforms, this tool streamlines scientific research by connecting AI analysis with verified experimental data.

Key Features

01Access to 4,200+ processed metabolomics studies and detailed metadata

02Mass spectrometry search capabilities by m/z ratio and ion adducts

03Integration of gene and protein-metabolite association data

04Metabolite nomenclature standardization using the RefMet database

05Retrieval of metabolite structures, identifiers (PubChem, KEGG), and classifications

061 GitHub stars

Use Cases

01Standardizing chemical nomenclature in research datasets to facilitate meta-analysis

02Identifying disease-specific metabolomics studies across different analytical platforms

03Automating metabolite identification from raw mass spectrometry m/z data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Download Skill