metabolomics-workbench-database

Metabolomics Workbench Database

Skill Overview

Access the NIH-funded Metabolomics Workbench via a REST API to retrieve 4,200+ metabolomics study datasets, supporting metabolite queries, mass spectrometry data searches, and biomarker discovery.

Applicable Scenarios

1. Acquisition of Metabolomics Study Data

Researchers can quickly retrieve and download public metabolomics study data via this skill, including experimental conditions, analysis results, and metadata—suitable for literature validation, secondary analysis, and cross-study comparison.

2. Metabolite Identification and Name Standardization

Use the RefMet database to standardize metabolite names and precisely match metabolites by m/z, chemical formula, or InChIKey, resolving inconsistent naming across databases and improving data integration efficiency.

3. Mass Spectrometry Data Analysis and Compound Identification

For MS data generated by LC-MS, GC-MS, and NMR platforms, use the m/z search function to rapidly identify candidate compounds, with support for multiple ion adduct types and mass tolerance settings.

Core Features

1. Metabolite Structure and Information Query

Supports retrieval of metabolite information using multiple identifiers (PubChem CID, InChIKey, KEGG ID, HMDB ID, etc.), allows downloading molecular structures (MOL/PNG), and provides compound classification and cross-database references.

2. Study Data and Metadata Access

Provides filtering of studies by metabolite, institution, researcher, or disease type, and returns study summaries, experimental factors, analytical methods, and full experimental data (supports JSON and TXT formats).

3. Mass Spec m/z Search

Supports searching compounds by mass-to-charge (m/z) values, allows specification of ion adduct types (M+H, M-H, M+Na, etc.) and mass tolerance, and searches matches across Metabolomics Workbench, LIPIDS, and RefMet databases.

Frequently Asked Questions

What is the Metabolomics Workbench?

It is a national metabolomics data repository funded by the NIH Common Fund and hosted by UCSD, containing over 4,200 curated metabolomics studies (more than 3,790 publicly available). It provides standardized metabolite naming and powerful search capabilities.

How do I use this API skill?

This skill offers REST API access. You can obtain data by sending HTTP requests to specific endpoints, for example to query compound information, search studies, or perform m/z searches. The API returns data in JSON or TXT formats and supports programmatic integration and automated data retrieval.

Is data access free?

Yes. Metabolomics Workbench is an open academic resource; all data and study results are freely accessible. API calls require no authentication, but it is recommended to use the service responsibly and cache commonly used reference data to reduce request frequency.