Can I search for metabolites using mass spectrometry data?

Yes, the skill supports m/z searches with specified ion adducts (like M+H or M-H) and adjustable mass tolerance across multiple databases.

How does it handle metabolite naming inconsistencies?

It uses the RefMet database to map common or synonymous metabolite names to a standardized nomenclature and systematic structural classification.

What analytical platforms are supported?

The skill provides data and metadata from studies utilizing LC-MS, GC-MS, and NMR analytical methods.

Can I retrieve gene and protein associations?

Yes, you can query associated genes and proteins related to metabolic pathways and specific metabolite metabolism directly through the API.

What data sources does this skill access?

It connects to the NIH Metabolomics Workbench hosted at UCSD, covering over 4,200 processed scientific studies and standardized metabolite repositories.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: K-Dense-AI

byK-Dense-AI

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3,719

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数据科学与机器学习

Accesses the NIH Metabolomics Workbench API to retrieve metabolite structures, study metadata, and standardized chemical nomenclature for biomarker discovery.

This skill integrates Claude with the NIH Common Fund-sponsored Metabolomics Workbench, enabling researchers and developers to programmatically query over 4,200 metabolomics studies. It facilitates the standardization of metabolite names via RefMet, performs mass spectrometry searches (m/z), and retrieves gene-protein-metabolite associations. Whether you are performing untargeted metabolomics analysis or searching for specific biomarker data across LC-MS, GC-MS, or NMR platforms, this skill provides the tools to navigate complex biochemical datasets directly within your AI workflow.

主要功能

01Search mass spectrometry data by mass-to-charge ratio (m/z) and specific ion adducts

02Filter metabolomics data by species, sample source, disease, and analytical method

033,719 GitHub stars

04Standardize chemical nomenclature using the RefMet database classification hierarchy

05Query metabolite structures and cross-reference IDs including PubChem, KEGG, and HMDB

06Access comprehensive study metadata, experimental factors, and raw analytical results

使用场景

01Standardizing metabolite lists to RefMet nomenclature for consistent multi-study analysis

02Automating the retrieval of experimental datasets for specific diseases like cancer or diabetes

03Identifying unknown compounds from mass spectrometry m/z values and adduct types

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Download Skill