Can I perform mass spectrometry searches with this skill?

Yes, you can search by mass-to-charge ratio (m/z) across multiple databases (LIPIDS, RefMet) while specifying ion adduct types like M+H or M-H and setting mass tolerance.

What is the NIH Metabolomics Workbench?

The Metabolomics Workbench is a comprehensive NIH-sponsored platform that serves as a repository for metabolomics research data, including studies, metabolite structures, and standardized nomenclature.

Does this skill provide access to genomic data?

The skill can retrieve gene and protein information specifically associated with metabolic pathways and metabolite metabolism through the Workbench's REST API.

How does this skill handle metabolite naming consistency?

It utilizes the RefMet database to map common metabolite names to standardized names across four structural resolution levels, ensuring consistency across different analytical platforms.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: x-cmd

byx-cmd

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数据科学与机器学习

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

This skill provides programmatic access to the NIH Metabolomics Workbench, a premier repository for metabolomics research data. It enables users to interface with over 4,200 processed studies, perform mass spectrometry (m/z) searches, and standardize metabolite nomenclature using the RefMet database. By integrating these capabilities into an AI coding environment, researchers and bioinformaticians can streamline the retrieval of experimental results, molecular structures, and gene-metabolite associations, significantly accelerating data analysis and biomarker discovery workflows.

主要功能

01REST API access to 4,200+ processed metabolomics studies

02Retrieval of molecular structures (MOL/PNG) and chemical properties

038 GitHub stars

04Cross-referencing for gene and protein-metabolite associations

05Mass spectrometry m/z searches with ion adduct and tolerance support

06Standardized nomenclature matching via the RefMet database

使用场景

01Identifying chemical compounds from experimental mass spectrometry results

02Automating the retrieval of experimental study metadata for comparative meta-analysis

03Standardizing metabolite names across large datasets to ensure data consistency

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill metabolomics-workbench-database

For use in Claude.ai and ChatGPT

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