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alterlab-metabolomics-wb

Query and consolidate metabolomics data from the Metabolomics Workbench REST API.

58|9|Updated Mar 16, 2026
Search Tags:#metabolomics#rest-api#mwtab#data-retrieval#refmet#moverz#study-data
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-metabolomics-wb
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-metabolomics-wb
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-metabolomics-wb
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-metabolomics-wb

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to comprehensive metabolomics data often requires manual API exploration and multiple endpoints; this skill streamlines programmatic retrieval from Metabolomics Workbench for researchers and data scientists.

Core Features & Use Cases

  • Query metabolite structures, study metadata, and mwTab data via REST endpoints.
  • Use RefMet to standardize metabolite nomenclature and cross-reference with KEGG, HMDB, and PubChem.
  • Retrieve gene and protein associations and perform targeted data pulls for meta-analyses or reproducible workflows.

Quick Start

Provide a concrete example request to fetch a study summary for ST000001 and iterate from there.

Frequently Asked Questions about alterlab-metabolomics-wb

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve metabolomics study metadata and experimental results from the Metabolomics Workbench API?▼

Retrieve metabolomics study data by querying the Metabolomics Workbench REST API using a study_id. The endpoint returns JSON or TXT outputs containing study metadata, experimental results, and mwTab data for analysis.

How do I standardize metabolite nomenclature using RefMet for cross-referencing databases?▼

Standardize metabolite names using the RefMet endpoint in the Metabolomics Workbench REST API. Provide a refmet_name identifier to cross-reference metabolites with KEGG, HMDB, and PubChem databases for consistent nomenclature.

Can I perform m/z searches to identify metabolites via the Metabolomics Workbench REST API?▼

Perform m/z searches using the moverz endpoint in the Metabolomics Workbench REST API. Input mass-to-charge ratios to query and identify matching metabolites, returning structured JSON or TXT output for downstream analysis.

What identifiers do I need to query compound and protein data from the Metabolomics Workbench?▼

Query compound and protein data using identifiers like regno, pubchem_cid, or study_id. The compound, gene, and protein endpoints process these inputs to return structured JSON or TXT metadata and association data.

What format are the outputs returned in when querying Metabolomics Workbench endpoints?▼

Outputs from Metabolomics Workbench REST API endpoints are returned in JSON or TXT format. This includes data from compound, study, refmet, metstat, moverz, gene, and protein endpoint queries.

Does this approach to metabolomics data retrieval require manual exploration of multiple API endpoints?▼

No, this approach streamlines programmatic retrieval from Metabolomics Workbench by consolidating access across compounds, studies, RefMet nomenclature, and related resources, eliminating the need for manual multi-endpoint API exploration.

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