Can I use this skill for commercial purposes?

While HMDB is a free resource for the public, commercial use of its data requires explicit permission from the original authors.

What is the HMDB Claude Code Skill?

It is a specialized capability for Claude that provides guidance and patterns for accessing the Human Metabolome Database, covering over 220,000 metabolites.

What types of data can I retrieve using this skill?

You can access chemical structures, clinical biomarker associations, normal concentration ranges in biofluids, and experimental NMR/MS spectral data.

Is this skill suitable for large-scale data analysis?

Yes, it provides best practices for bulk data downloads and integration with data science pipelines for high-throughput metabolomics workflows.

Does this skill provide a direct REST API?

HMDB does not have a public REST API; this skill provides guidance on programmatic access through R packages or local parsing of bulk XML/CSV datasets.

HMDB Metabolome Database

Name: HMDB Metabolome Database
Author: Sologa

bySologa

Data Science & ML

Accesses and queries the Human Metabolome Database for detailed metabolite information, clinical biomarkers, and biochemical pathways.

About

The HMDB Database skill enables seamless integration with the world's most comprehensive resource for human small molecule metabolites. It allows researchers and developers to perform complex searches across over 220,000 metabolites, retrieve detailed chemical properties, biological context, and clinical biomarker data. Ideal for metabolomics research, drug discovery, and clinical chemistry, this skill provides structured guidance on navigating the HMDB ecosystem, identifying compounds through spectral matching, and leveraging bulk datasets for advanced data science workflows.

Key Features

Guidance on bulk data downloads and programmatic access via R/Bioconductor
Comprehensive metabolite search by name, ID, or chemical structure (SMILES/InChI)
0 GitHub stars
Access to detailed biochemical pathways and enzymatic reaction data
Retrieval of clinical biomarker data and normal/abnormal concentration ranges
Integration with spectroscopic data for NMR and MS-MS metabolite identification

Use Cases

Discovering and validating biomarkers for clinical disease associations
Mapping metabolite lists to biological pathways and enzymatic networks
Identifying unknown metabolites in untargeted metabolomics research

About

Key Features

Guidance on bulk data downloads and programmatic access via R/Bioconductor
Comprehensive metabolite search by name, ID, or chemical structure (SMILES/InChI)
0 GitHub stars
Access to detailed biochemical pathways and enzymatic reaction data
Retrieval of clinical biomarker data and normal/abnormal concentration ranges
Integration with spectroscopic data for NMR and MS-MS metabolite identification

Use Cases

Discovering and validating biomarkers for clinical disease associations
Mapping metabolite lists to biological pathways and enzymatic networks
Identifying unknown metabolites in untargeted metabolomics research