skills.rest
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hmdb-database

Fetch HMDB metabolite records by accession via REST endpoints.

7|Updated Apr 5, 2026
Search Tags:#database#rest#metabolomics#pathways#hmdb#cross-references#diseases
One-click install
npx skills add https://github.com/dailycafi/metabolism-skills --skill hmdb-database-dailycafi
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hmdb-database
Source: https://github.com/dailycafi/metabolism-skills/tree/main/skills/databases/hmdb
Command: npx skills add https://github.com/dailycafi/metabolism-skills --skill hmdb-database-dailycafi

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

HMDB is a comprehensive human metabolite database; this skill provides programmatic access to look up metabolites, retrieve details, pathways, and disease associations via REST endpoints, enabling research workflows without manual browsing.

Core Features & Use Cases

  • Retrieve detailed metabolite records by HMDB accession (e.g., HMDB0000122) including chemical formula, mass, SMILES, and InChIKey.
  • Extract cross-references (KEGG, PubChem, ChEBI, DrugBank, etc.) and connect metabolites to pathways and diseases.
  • Batch lookups and simple name/mass-based search workflows to support MS/NMR metabolomics exploration.

Quick Start

Query HMDB with an accession to fetch a full metabolite record and cross references.

Frequently Asked Questions about hmdb-database

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

FAQPage Schema
How do I retrieve HMDB metabolite data using an accession ID?▼

To retrieve HMDB metabolite data, query the REST endpoint with a specific accession ID like HMDB0000122. This fetches comprehensive records including chemical formula, mass, SMILES, and InChIKey.

What metabolite cross-references can I extract from HMDB?▼

You can extract cross-references from HMDB to external databases such as KEGG, PubChem, ChEBI, and DrugBank. This connects metabolite records to broader chemical and biological database identifiers.

Can I connect HMDB metabolites to biological pathways and disease associations?▼

Yes, HMDB metabolite lookups include pathway and disease association data. This enables metabolite-centric research workflows by linking chemical compounds directly to their biological and clinical contexts.

Does this HMDB REST tool support batch lookups and name or mass-based searches?▼

Yes, the tool supports batch lookups and simple name or mass-based search workflows. This functionality specifically supports MS and NMR metabolomics exploration by allowing multi-metabolite retrieval.

What is the best way to handle REST rate limiting when fetching HMDB metabolite records?▼

The best way to handle REST rate limiting is using this Python-based data retrieval tool, which includes proper headers and rate handling logic to manage HMDB API requests and optional bulk data downloads.

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