Is there a public REST API for HMDB?

HMDB does not provide a standard public REST API. This skill provides instructions on how to request programmatic access or use the hmdbQuery R/Bioconductor package.

Can I download HMDB data for local analysis?

Yes, the skill provides information on how to retrieve bulk datasets in XML, SDF, and CSV formats for integration into local data analysis pipelines.

Does this skill provide spectral data for compound identification?

Yes, it assists in accessing reference NMR, MS, and MS-MS spectra to help identify metabolites found in experimental samples.

Can I search the HMDB by chemical structure using this skill?

Yes, this skill supports guidance for searching via chemical representations like SMILES or InChI strings to find specific metabolites within the database.

Is HMDB data free for commercial use?

HMDB is free for academic and non-commercial research; however, commercial organizations require explicit permission from the development team.

HMDB Database Assistant

Name: HMDB Database Assistant
Author: Microck

byMicrock

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Data Science & ML

Accesses the Human Metabolome Database to retrieve metabolite properties, clinical biomarker data, and spectral information for metabolomics research.

This skill empowers Claude to interact with the Human Metabolome Database (HMDB), a massive repository containing over 220,000 human metabolites. It streamlines complex research workflows by enabling searches for compounds via name, ID, structure, or spectral data, while providing deep biological context including pathway associations and clinical biomarker data. Whether performing untargeted metabolomics identification or investigating disease-specific chemical concentrations, this tool serves as a bridge between AI-assisted coding and high-fidelity biochemical data.

Key Features

0181 GitHub stars

02Retrieval of biological context including metabolic pathways and enzyme associations

03Guidance on programmatic data access via XML, SDF, and R/Bioconductor packages

04Access to clinical data including disease associations and normal concentration ranges

05Integration with spectral data (NMR, MS, MS-MS) for compound identification

06Comprehensive metabolite search by name, HMDB ID, SMILES, or InChI strings

Use Cases

01Mapping metabolite lists to metabolic pathways for biological interpretation and enrichment analysis

02Identifying unknown metabolites in untargeted metabolomics studies using spectral matching

03Researching clinical biomarkers and their associated concentration ranges in human biological fluids

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills hmdb-database

For use in Claude.ai and ChatGPT

Download Skill