Can I filter studies by specific diseases or sample types?

Yes, using the MetStat context, you can filter studies by analytical platform, species, sample source (e.g., Blood), and specific diseases like Diabetes or Cancer.

How does it handle mass spectrometry searches?

It allows you to search by m/z values across multiple databases, specifying ion adduct types (like M+H or M-H) and defining mass tolerance for precise matching.

Is the data returned in a machine-readable format?

The skill primarily retrieves data in JSON format via the REST API, making it ideal for further analysis, visualization, or integration into data science pipelines.

What kind of data can I retrieve with the Metabolomics Workbench skill?

You can access metadata and results for over 4,200 studies, metabolite structures, standardized RefMet nomenclature, and gene-protein-metabolite associations.

Why should I use RefMet for nomenclature standardization?

RefMet provides a standardized naming convention and hierarchical classification for metabolites, ensuring consistency across different experimental datasets.

Metabolomics Workbench Database

Name: Metabolomics Workbench Database
Author: Yezez9

byYezez9

0•

数据科学与机器学习

Facilitates programmatic access to the NIH Metabolomics Workbench for metabolite profiling, biomarker discovery, and experimental data retrieval.

This skill provides a specialized interface for the NIH Common Fund-sponsored Metabolomics Workbench, the primary repository for metabolomics research data. It enables researchers to programmatically query over 4,200 studies, standardize chemical nomenclature via RefMet, and perform mass spectrometry searches using m/z values. By integrating with the workbench's REST API, the skill streamlines the discovery of metabolite structures, gene-protein associations, and experimental metadata, making it an essential tool for bioinformatics, drug discovery, and clinical research workflows within Claude Code.

主要功能

01Comprehensive cross-referencing across PubChem, KEGG, HMDB, and RefSeq

020 GitHub stars

03High-precision mass spectrometry searches using m/z values and specific ion adducts

04Standardized metabolite nomenclature via integrated RefMet database matching

05Programmatic access to 4,200+ metabolomics studies and raw experimental data

06Filtering by analytical methods (LC-MS, GC-MS, NMR) and biological parameters

使用场景

01Standardizing metabolite lists for comparative study across different research labs

02Extracting disease-specific metabolic signatures for biomarker discovery and clinical research

03Identifying unknown compounds from mass spectrometry data during chemical analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent metabolomics-workbench-database

For use in Claude.ai and ChatGPT

主要功能

01Comprehensive cross-referencing across PubChem, KEGG, HMDB, and RefSeq

020 GitHub stars

03High-precision mass spectrometry searches using m/z values and specific ion adducts

04Standardized metabolite nomenclature via integrated RefMet database matching

05Programmatic access to 4,200+ metabolomics studies and raw experimental data

06Filtering by analytical methods (LC-MS, GC-MS, NMR) and biological parameters

使用场景

01Standardizing metabolite lists for comparative study across different research labs

02Extracting disease-specific metabolic signatures for biomarker discovery and clinical research

03Identifying unknown compounds from mass spectrometry data during chemical analysis