Does it handle study IDs from Metabolomics Workbench?

Yes, it automatically detects and processes study IDs starting with 'ST' for Metabolomics Workbench and 'MTBLS' for MetaboLights.

What metabolite identifiers are supported?

The skill accepts common names and provides HMDB IDs, PubChem CIDs, SMILES, and molecular formulas in its reports.

Which databases does this skill search?

It integrates HMDB for metabolites, MetaboLights and Metabolomics Workbench for studies, and PubChem for fallback chemical data.

How are the research results delivered?

The skill generates a structured Markdown report containing metabolite annotations, study details, and database statistics for easy sharing and review.

Can I search for studies by specific diseases?

Yes, you can use keyword searches like 'diabetes' or 'cancer' to find relevant metabolomics studies across multiple repositories.

Metabolomics Research Assistant

Name: Metabolomics Research Assistant
Author: mims-harvard

bymims-harvard

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1,150

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データサイエンスとML

Facilitates metabolomics research by identifying metabolites and retrieving detailed study data from HMDB, MetaboLights, and Metabolomics Workbench.

This skill provides a comprehensive research pipeline for metabolomics, enabling users to automatically annotate metabolites with HMDB IDs, chemical properties, and biological pathways. It seamlessly integrates multiple scientific databases including MetaboLights and Metabolomics Workbench to search for and retrieve detailed study metadata, experimental designs, and data availability. Whether you're performing metabolite profiling or searching for existing studies related to specific diseases, this skill automates the data collection process and generates structured markdown reports for scientific analysis.

主な機能

01Multi-database metabolite identification using HMDB and PubChem fallbacks

02Advanced study searching by keyword, disease, or organism filters

03Intelligent fallback strategies for robust chemical and biological data acquisition

041,150 GitHub stars

05Generation of structured, production-ready markdown research reports

06Automated study metadata retrieval from MetaboLights (MTBLS) and Metabolomics Workbench (ST)

ユースケース

01Retrieving comprehensive experimental design and metadata for specific study identifiers

02Searching for metabolomics studies related to specific pathologies like diabetes or cancer

03Annotating metabolite lists with HMDB IDs, pathways, and chemical formulas

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add mims-harvard/tooluniverse tooluniverse-metabolomics

For use in Claude.ai and ChatGPT

Download Skill