Can I use HMDB data for commercial research?

HMDB is free for academic and non-commercial research; however, commercial organizations must contact the HMDB team for explicit permission.

What is the HMDB Claude Code Skill?

It is a specialized capability that allows Claude to assist with searching, analyzing, and integrating data from the Human Metabolome Database (HMDB) for research and development.

Can I search for metabolites by chemical structure?

Yes, the skill provides guidance on performing structure-based searches using SMILES or InChI strings via HMDB's ChemQuery interface.

Does this skill provide NMR and MS spectra data?

Yes, it allows you to retrieve reference peaks and spectroscopic data for both experimental and predicted NMR, MS, and MS-MS spectra.

Is there an API for programmatic access to HMDB?

While HMDB lacks a public REST API, this skill provides instructions for obtaining authorized API access for research or using R/Bioconductor packages like hmdbQuery.

HMDB Metabolome Database Access

Name: HMDB Metabolome Database Access
Author: Microck

byMicrock

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Data Science & ML

Accesses and analyzes the Human Metabolome Database to retrieve metabolite data, chemical properties, and clinical biomarkers.

About

This skill integrates the Human Metabolome Database (HMDB) into the Claude environment, providing comprehensive access to over 220,000 metabolite entries. It enables researchers and developers to perform structure-based searches, retrieve spectroscopic data (NMR/MS), and analyze biological pathways or clinical biomarkers. Whether you are identifying unknown metabolites in untargeted metabolomics or exploring the clinical significance of specific small molecules, this skill provides the domain-specific guidance and implementation patterns needed to leverage HMDB's vast repository of human metabolic information.

Key Features

Search metabolites by name, ID, SMILES, or InChI structure
Analyze metabolic pathways and biological locations
81 GitHub stars
Retrieve chemical properties, formulas, and molecular weights
Access clinical biomarker associations and disease data
Guidance on bulk data downloads and programmatic API access

Use Cases

Discovering biomarkers for clinical research and disease profiling
Integrating human metabolic data into bioinformatics pipelines
Identifying metabolites from experimental NMR or MS spectra

About

Key Features

Search metabolites by name, ID, SMILES, or InChI structure
Analyze metabolic pathways and biological locations
81 GitHub stars
Retrieve chemical properties, formulas, and molecular weights
Access clinical biomarker associations and disease data
Guidance on bulk data downloads and programmatic API access

Use Cases

Discovering biomarkers for clinical research and disease profiling
Integrating human metabolic data into bioinformatics pipelines
Identifying metabolites from experimental NMR or MS spectra