What is the HMDB Claude Code Skill used for?

It is used to query the Human Metabolome Database for chemical, clinical, and molecular information about small molecule metabolites found in the human body.

Does this skill provide spectral data for identification?

Yes, it provides access to experimental and predicted NMR, MS, and MS-MS spectra to help identify metabolites in untargeted metabolomics workflows.

Is the data in the HMDB skill up to date?

The skill provides guidance based on HMDB version 5.0 (2025), which includes the most current metabolite and protein sequence data available.

Can I perform structure searches with this skill?

Yes, the skill supports searches via SMILES, InChI strings, and molecular weight ranges to find specific chemical compounds.

HMDB Metabolomics Database

Name: HMDB Metabolomics Database
Author: Activer007

byActiver007

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Data Science & ML

Provides comprehensive access to the Human Metabolome Database (HMDB) for metabolite identification, biomarker discovery, and clinical chemistry research.

The HMDB Metabolomics Database skill empowers Claude to assist with complex biochemical and clinical research by accessing over 220,000 metabolite entries. It facilitates metabolite identification through spectral matching (NMR/MS), chemical property retrieval, and the exploration of biological pathways. This skill is particularly useful for researchers performing untargeted metabolomics, studying disease biomarkers, or integrating chemical taxonomy and clinical data into their scientific workflows, offering detailed information on both water-soluble and lipid-soluble compounds found in the human body.

Key Features

01Spectral matching capabilities for LC-MS, GC-MS, and NMR identification

02Access to 220,000+ metabolite entries and 8,600+ protein sequences

03Detailed clinical data including biomarker associations and concentration ranges

04Integration with biological pathways and external databases like KEGG and PubChem

050 GitHub stars

06Support for structure-based searches using SMILES, InChI, and ChemQuery

Use Cases

01Discovering clinical biomarkers by correlating metabolite concentrations with disease states

02Mapping metabolic pathways and enzymatic reactions for biological interpretation

03Identifying unknown metabolites from experimental MS or NMR spectral data

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills hmdb-database

For use in Claude.ai and ChatGPT

Download Skill