What is the Metabolomics Workbench?

The Metabolomics Workbench is an NIH Common Fund-sponsored platform hosted at UCSD that serves as a national repository for metabolomics research data, providing access to thousands of studies across various analytical platforms.

What data formats does the Metabolomics Workbench API return?

The API primarily returns JSON for programmatic integration but also supports TXT for human-readable tab-delimited data, as well as MOL and PNG files for molecular structures.

Can I search for metabolites by mass using this skill?

Yes, the skill supports searching by mass-to-charge ratio (m/z) with specified ion adducts (like M+H or M-H) and customizable mass tolerance across several databases including RefMet and LIPIDS.

Does this skill help with metabolite naming consistency?

Absolutely. It utilizes the RefMet database to standardize metabolite nomenclature, allowing you to map common or ambiguous names to a systematic, hierarchical classification.

Metabolomics Workbench Explorer

Name: Metabolomics Workbench Explorer
Author: Sologa

bySologa

0•

Data Science & ML

Accesses the NIH Metabolomics Workbench REST API to retrieve comprehensive metabolomics study data, metabolite structures, and standardized RefMet nomenclature.

This skill provides programmatic access to the Metabolomics Workbench, the primary NIH-sponsored repository for metabolomics research. It enables users to query over 4,200 processed studies, perform mass spectrometry searches by m/z values, and standardize chemical nomenclature using the RefMet database. Whether you are conducting biomarker discovery, cross-referencing metabolites across external databases like PubChem and KEGG, or retrieving experimental metadata for bioinformatics pipelines, this skill streamlines the integration of high-quality metabolomics data into your Claude-powered workflows.

Key Features

01Standardized metabolite nomenclature and hierarchical classification via RefMet

02Cross-referencing for gene and protein associations related to metabolic pathways

030 GitHub stars

04Molecular structure retrieval in MOL and PNG formats using various chemical identifiers

05Mass spectrometry m/z searching with support for specific ion adducts and mass tolerance

06Programmatic access to 4,200+ metabolomics studies and raw experimental data

Use Cases

01Standardizing diverse metabolite names in datasets to a consistent nomenclature for data cleaning

02Automating the retrieval of experimental datasets for large-scale meta-analysis and research surveys

03Identifying potential chemical compounds from mass spectrometry precursor ion data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline metabolomics-workbench-database

For use in Claude.ai and ChatGPT

Download Skill