Is there a public REST API for HMDB?

HMDB does not have a standard public REST API; however, this skill provides information on obtaining programmatic access through the development team or using the hmdbQuery R package.

Can I search for metabolites by chemical structure?

Yes, the skill supports structure-based search patterns using SMILES, InChI, and molecular weight ranges.

Does this skill provide spectroscopic data?

It provides access to both experimental and predicted NMR and MS spectra, which are crucial for metabolite identification in research.

What version of HMDB does this skill support?

This skill provides guidance and patterns for HMDB version 5.0 (2025), which includes over 220,000 metabolite entries.

HMDB Database Explorer

Name: HMDB Database Explorer
Author: ricable

byricable

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Data Science & ML

Accesses the Human Metabolome Database (HMDB) to retrieve metabolite data, chemical properties, and clinical biomarkers for metabolomics research.

About

The HMDB Database skill integrates the Human Metabolome Database into the Claude environment, providing specialized access to over 220,000 metabolite entries. It enables researchers and developers to perform structure-based searches, retrieve spectroscopic data (NMR/MS), and analyze metabolic pathways directly within their AI-assisted workflows. This skill is essential for tasks involving clinical chemistry, biomarker discovery, and metabolite identification, offering guidance on data retrieval, programmatic access via R/Bioconductor, and bulk dataset parsing for advanced scientific analysis.

Key Features

Access experimental and predicted NMR, GC-MS, and MS-MS spectra
Retrieve clinical biomarker data and normal/abnormal concentration ranges
Guidance for bulk data processing using XML, SDF, and CSV formats
1 GitHub stars
Map metabolites to biological pathways, enzymes, and transporters
Search 220K+ metabolites by name, HMDB ID, SMILES, or InChI strings

Use Cases

Identifying unknown metabolites in untargeted metabolomics workflows
Building cheminformatics pipelines that require high-fidelity human metabolite data
Automating biomarker discovery for clinical research and disease profiling

About

Key Features

Access experimental and predicted NMR, GC-MS, and MS-MS spectra
Retrieve clinical biomarker data and normal/abnormal concentration ranges
Guidance for bulk data processing using XML, SDF, and CSV formats
1 GitHub stars
Map metabolites to biological pathways, enzymes, and transporters
Search 220K+ metabolites by name, HMDB ID, SMILES, or InChI strings

Use Cases

Identifying unknown metabolites in untargeted metabolomics workflows
Building cheminformatics pipelines that require high-fidelity human metabolite data
Automating biomarker discovery for clinical research and disease profiling