What kind of clinical data is available?

The skill can retrieve clinical significance data, including metabolite concentrations in different biofluids (urine, serum, etc.) and associations with specific diseases.

Is an API key required to use this skill?

Standard web-based queries and data retrieval do not require an API key, though high-volume programmatic access may require contacting the HMDB development team.

Does this provide spectral data for identification?

Yes, it provides access to experimental and predicted NMR, MS, and MS-MS spectra, which are essential for identifying compounds in metabolomics workflows.

What is the HMDB Database skill?

The HMDB Database skill is a specialized capability for Claude that allows it to query the Human Metabolome Database to find detailed information on 220,000+ metabolites found in the human body.

Can I search by chemical structure?

Yes, the skill supports structure-based searches, including substructure queries using SMILES strings, InChI, or molecular weight ranges.

HMDB Database Access

Name: HMDB Database Access
Author: x-cmd

byx-cmd

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Data Science & ML

Accesses the Human Metabolome Database (HMDB) to retrieve detailed information on over 220,000 human metabolites, including chemical properties, clinical biomarkers, and spectral data.

About

This skill empowers Claude to interact with the Human Metabolome Database (HMDB), the world's most comprehensive resource for human small molecule metabolites. It enables researchers and developers to perform deep queries across chemical structures, biological pathways, and clinical concentrations. Whether you are identifying unknown metabolites from NMR/MS spectra, exploring disease-associated biomarkers, or mapping metabolic pathways, this skill provides the domain-specific logic needed to navigate HMDB's 220,000+ entries and extensive clinical datasets effectively for metabolomics research and clinical chemistry.

Key Features

Map metabolites to biological pathways and associated enzymes or transporters
Retrieve detailed chemical properties including SMILES, InChI, and molecular weight
Reference experimental and predicted NMR, MS, and MS-MS spectra
Search 220K+ metabolites by name, HMDB ID, or chemical structure
Access clinical biomarker data and normal/abnormal concentration ranges
8 GitHub stars

Use Cases

Cheminformatics workflows requiring structured human metabolic data and taxonomy
Metabolite identification in untargeted metabolomics using experimental spectra
Clinical biomarker discovery for disease association and concentration analysis

About

Key Features

Map metabolites to biological pathways and associated enzymes or transporters
Retrieve detailed chemical properties including SMILES, InChI, and molecular weight
Reference experimental and predicted NMR, MS, and MS-MS spectra
Search 220K+ metabolites by name, HMDB ID, or chemical structure
Access clinical biomarker data and normal/abnormal concentration ranges
8 GitHub stars

Use Cases

Cheminformatics workflows requiring structured human metabolic data and taxonomy
Metabolite identification in untargeted metabolomics using experimental spectra
Clinical biomarker discovery for disease association and concentration analysis