How does this skill help with mass spectrometry?

It allows you to search for compounds by mass-to-charge ratio (m/z) across multiple databases using specific ion adducts and mass tolerances to identify potential metabolites.

Can I standardize metabolite names with this skill?

Yes, it uses the RefMet database to map common or non-standard metabolite names to standardized nomenclature and hierarchical chemical classifications.

What data formats are supported by this skill?

The skill interacts with the Metabolomics Workbench REST API to retrieve data in both machine-readable JSON and human-readable tab-delimited TXT formats.

What is the Metabolomics Workbench?

The Metabolomics Workbench is an NIH-sponsored repository providing data from over 4,200 metabolomics studies, including metabolites, experimental factors, and analytical results.

Metabolomics Workbench Database Explorer

Name: Metabolomics Workbench Database Explorer
Author: Zehong-Wang

byZehong-Wang

0•

데이터 과학 및 ML

Accesses the NIH Metabolomics Workbench REST API to query metabolite data, study metadata, and perform mass spectrometry searches.

The Metabolomics Workbench Database skill provides programmatic access to the NIH Common Fund-sponsored repository, hosting over 4,200 metabolomics studies. It enables researchers to standardize metabolite nomenclature via RefMet, perform mass-to-charge (m/z) searches for compound identification, and retrieve detailed experimental results across GC-MS, LC-MS, and NMR platforms. This skill is essential for biomarker discovery, metabolic pathway analysis, and integrating multi-omics data by bridging the gap between raw study data and actionable chemical insights directly within the Claude environment.

주요 기능

010 GitHub stars

02Perform m/z searches with specified ion adducts and tolerances

03Standardize nomenclature using the RefMet database

04Retrieve metabolite structures, identifiers, and cross-references

05Query 4,200+ metabolomics studies and experimental metadata

06Access gene and protein associations for metabolic pathways

사용 사례

01Comparing experimental results across multiple public metabolomics studies

02Identifying unknown compounds from mass spectrometry m/z values

03Standardizing disparate metabolite names for meta-analysis using RefMet

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Download Skill