How does RefMet standardization work in this skill?

RefMet is used to map common metabolite names to a standardized nomenclature and hierarchical classification, ensuring consistent data retrieval across different research studies.

Can I use this skill to identify metabolites from MS data?

Yes, the skill supports searching by mass-to-charge ratio (m/z) with specific ion adducts (like M+H or M-H) and custom mass tolerance levels to identify potential compound matches.

Is gene and protein information available through this skill?

Yes, the skill can retrieve gene and protein data associated with specific metabolic pathways, including UniProt IDs, protein sequences, and gene symbols.

What is the primary function of the Metabolomics Workbench skill?

It provides a programmatic interface to the NIH Metabolomics Workbench, allowing users to search metabolites, access experimental study data, and standardize nomenclature via the RefMet database.

What types of analytical platforms can I filter by?

You can filter metabolomics studies by various analytical methods including LC-MS, GC-MS, and NMR, as well as by ionization polarity and chromatography types.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: Activer007

byActiver007

データサイエンスとML

Accesses the NIH Metabolomics Workbench to query metabolite structures, experimental studies, and mass spectrometry data.

概要

The Metabolomics Workbench Database skill provides programmatic access to the NIH Common Fund's primary repository for metabolomics research. It allows researchers and developers to query over 4,200 processed studies, retrieve standardized metabolite nomenclature through RefMet, and perform high-precision mass spectrometry searches (m/z). This skill is essential for bioinformatics workflows, biomarker discovery, and cross-referencing metabolic data with external databases like PubChem, KEGG, and HMDB, making it a powerful tool for life science data analysis.

主な機能

Perform mass spectrometry m/z searches with specific ion adducts
Filter over 4,200 studies by disease, species, and analytical platform
0 GitHub stars
Standardize metabolite nomenclature using the RefMet hierarchical system
Query metabolite structures by PubChem CID, InChI Key, or KEGG ID
Access gene and protein associations for metabolic pathways

ユースケース

Automating the retrieval of study metadata for biomarker discovery research
Standardizing metabolite names across diverse datasets for meta-analysis
Identifying compounds from experimental mass spectrometry m/z values

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Download Skill

GitHub

概要