How does this skill help with mass spectrometry?

It allows you to search for compounds based on mass-to-charge (m/z) ratios, specific ion adducts (like M+H or M-H), and user-defined mass tolerance levels.

Does it provide access to molecular structures?

Yes, it can retrieve detailed compound data and download molecular structures as MOL files or PNG images using various identifiers like PubChem CID or InChI Key.

What is the Metabolomics Workbench?

It is an NIH-sponsored repository for metabolomics research data, hosting over 4,200 studies and standardized metabolite information for the scientific community.

Can I standardize metabolite names using this tool?

Yes, the skill leverages the RefMet database to map common or ambiguous metabolite names to standardized, systematic nomenclature across multiple structural levels.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: Microck

byMicrock

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Data Science & ML

Accesses and queries the NIH Metabolomics Workbench to retrieve study data, standardize nomenclature, and perform mass spectrometry searches.

This skill integrates Claude with the NIH Metabolomics Workbench REST API, providing programmatic access to over 4,200 metabolomics studies and comprehensive metabolite data. It enables researchers to standardize metabolite nomenclature using RefMet, perform mass spectrometry searches via m/z ratios, and retrieve experimental results across various platforms like GC-MS, LC-MS, and NMR. Whether you need to cross-reference compound identifiers, fetch molecular structures, or filter studies by biological parameters, this skill streamlines the process of biomarker discovery and metabolomics data analysis.

Key Features

01MetStat filtering by analytical method, species, and disease

02Cross-referencing between PubChem, KEGG, HMDB, and RefMet

03Standardized metabolite nomenclature using RefMet mapping

04Retrieval of study metadata and raw experimental datasets

0581 GitHub stars

06Mass spectrometry searching by m/z ratio and ion adducts

Use Cases

01Standardizing heterogeneous metabolite lists into a common nomenclature for publication

02Aggregating experimental results from clinical metabolomics studies for meta-analysis

03Identifying potential compounds from mass spectrometry m/z values during data analysis

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