Does HMDB require a license for commercial use?

HMDB is free for academic and non-commercial research, but commercial organizations should contact the HMDB team at the University of Alberta for permission.

Can I search for metabolites using chemical structures?

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

Is this tool suitable for clinical biomarker research?

Absolutely. It can retrieve normal and abnormal concentration ranges for metabolites in various biological fluids like urine, serum, and CSF.

What version of HMDB does this skill cover?

This skill is optimized for HMDB version 5.0, which includes over 220,945 metabolite entries and extensive spectral data.

Does this skill support programmatic database access?

Yes, it provides instructions for using the hmdbQuery R/Bioconductor package and parsing bulk XML/SDF datasets for automated workflows.

Human Metabolome Database (HMDB) Access

Name: Human Metabolome Database (HMDB) Access
Author: ovachiever

byovachiever

•

Data Science & ML

Accesses and analyzes data from the Human Metabolome Database for metabolite identification, biomarker discovery, and clinical research.

About

This skill empowers Claude to interact with the Human Metabolome Database (HMDB), a comprehensive resource containing over 220,000 metabolite entries found in the human body. It enables users to perform sophisticated searches by name, chemical structure, or spectral data, while providing deep biological context including pathway associations, clinical biomarker data, and physiological concentrations. This tool is essential for researchers in metabolomics, clinical chemistry, and bioinformatics who need to identify small molecules and understand their roles in human health and disease.

Key Features

Access experimental and predicted NMR, GC-MS, and LC-MS spectra
Guidance on bulk data processing and programmatic R/Bioconductor integration
Search over 220,000 metabolite entries by name, ID, SMILES, or InChI
5 GitHub stars
Analyze metabolic pathways and enzymatic reaction context
Retrieve detailed clinical biomarker associations and disease data

Use Cases

Mapping experimental results to biological pathways and specimens
Identifying unknown compounds in untargeted metabolomics experiments
Investigating clinical biomarkers and disease-related metabolic signatures

About

Key Features

Access experimental and predicted NMR, GC-MS, and LC-MS spectra
Guidance on bulk data processing and programmatic R/Bioconductor integration
Search over 220,000 metabolite entries by name, ID, SMILES, or InChI
5 GitHub stars
Analyze metabolic pathways and enzymatic reaction context
Retrieve detailed clinical biomarker associations and disease data

Use Cases

Mapping experimental results to biological pathways and specimens
Identifying unknown compounds in untargeted metabolomics experiments
Investigating clinical biomarkers and disease-related metabolic signatures