Does this skill provide direct API access to HMDB?

The skill provides guidance on utilizing the web interface, R/Bioconductor packages, and bulk downloads, as HMDB requires specific contact for authorized API access.

Is the clinical data in this skill reliable for research?

The skill references HMDB 5.0, which includes peer-reviewed clinical data, normal/abnormal concentration ranges, and disease-associated biomarkers.

What is the HMDB Claude Code Skill used for?

It is used to assist researchers in searching and interpreting data from the Human Metabolome Database, covering metabolite properties, clinical biomarkers, and spectral data.

Can I search for metabolites using chemical structures?

Yes, the skill helps you perform structure and substructure searches using SMILES or InChI strings via the HMDB ChemQuery interface.

HMDB Scientific Database Access

Name: HMDB Scientific Database Access
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Access and interpret the Human Metabolome Database for metabolite identification, biomarker discovery, and clinical chemistry research.

About

This skill integrates the Human Metabolome Database (HMDB) into Claude's workflow, enabling detailed queries across over 220,000 metabolite entries. It facilitates complex searches based on chemical structure, identifiers, and spectral data while providing access to clinical biomarkers, metabolic pathways, and spectroscopic references. Ideal for researchers in metabolomics and clinical chemistry, the skill streamlines the process of identifying compounds and understanding their biological roles within the human body by providing structured access to chemical, biological, and clinical data.

Key Features

Advanced search support for metabolites using names, IDs, or chemical structures (SMILES/InChI)
Access to clinical context including biomarker associations and biological concentrations
Guidance for bulk dataset downloads and programmatic access via XML, SDF, and R packages
1 GitHub stars
Retrieval of detailed chemical properties including taxonomy, molecular weight, and formulas
Spectroscopic matching support for NMR and MS-MS data interpretation

Use Cases

Identifying unknown metabolites in untargeted metabolomics from experimental MS/NMR spectra
Discovering and validating metabolite biomarkers for specific disease states
Mapping metabolic pathways and enzymatic reactions for biological interpretation

About

Key Features

Advanced search support for metabolites using names, IDs, or chemical structures (SMILES/InChI)
Access to clinical context including biomarker associations and biological concentrations
Guidance for bulk dataset downloads and programmatic access via XML, SDF, and R packages
1 GitHub stars
Retrieval of detailed chemical properties including taxonomy, molecular weight, and formulas
Spectroscopic matching support for NMR and MS-MS data interpretation

Use Cases

Identifying unknown metabolites in untargeted metabolomics from experimental MS/NMR spectra
Discovering and validating metabolite biomarkers for specific disease states
Mapping metabolic pathways and enzymatic reactions for biological interpretation