How do I use HMDB data programmatically with this skill?

The skill provides guidance on using the hmdbQuery R package and instructions for parsing bulk XML, SDF, or CSV downloads for integration into custom data pipelines.

What kind of data can I retrieve using the HMDB skill?

You can access chemical properties, structural identifiers like SMILES and InChI, spectral peak lists (NMR/MS), metabolic pathways, and clinical concentration data for over 220,000 human metabolites.

Is the data provided by this skill up to date?

The skill references HMDB version 5.0 (2023-2025 data), which is the most current major release containing updated metabolite entries and protein sequences.

Does it support clinical biomarker research?

Absolutely. The skill provides access to biomarker associations, disease-specific metabolic roles, and normal vs. abnormal concentration ranges in biofluids like serum, urine, and CSF.

Can this skill help with compound identification?

Yes, it provides methods for spectral matching and structure-based searches (including molecular weight and substructure) to help identify unknown metabolites from experimental data.

Human Metabolome Database Explorer

Name: Human Metabolome Database Explorer
Author: jackspace

byjackspace

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Data Science & ML

Accesses the Human Metabolome Database (HMDB) to retrieve detailed chemical properties, biomarker data, and spectral information for over 220,000 metabolites.

The Human Metabolome Database Explorer skill empowers Claude to navigate and utilize the HMDB, the world's most comprehensive resource for small molecule metabolites found in the human body. It facilitates advanced scientific workflows by providing structured access to chemical structures (SMILES/InChI), metabolic pathways, NMR/MS spectra, and clinical biomarker data. Ideal for researchers in metabolomics, clinical chemistry, and drug discovery, this skill helps identify unknown compounds, map disease-specific metabolic changes, and integrate high-fidelity biological data into research pipelines.

Key Features

01Access to experimental and predicted NMR, GC-MS, and LC-MS/MS spectral data

02Comprehensive search of 220,000+ metabolite entries including water- and lipid-soluble compounds

03Chemical property retrieval including structures, formulas, molecular weights, and taxonomy

04Clinical relevance mapping including biomarker associations and biofluid concentration ranges

05Guidance on bulk data integration using XML, SDF, and R-based programmatic tools

062 GitHub stars

Use Cases

01Investigating clinical biomarkers and metabolic pathways associated with specific human diseases

02Identifying unknown metabolites in untargeted metabolomics research through spectral matching and structural analysis

03Automating the collection of chemical identifiers and metabolic reactions for bioinformatics database construction

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jackspace/claudeskillz scientific-db-hmdb-database

For use in Claude.ai and ChatGPT

Download Skill