What data can I access through the HMDB skill?

You can access chemical properties, clinical biomarker data, biological pathways, and spectroscopic data (NMR/MS) for over 220,000 metabolites found in the human body.

Can this skill perform structure-based searches?

Yes, the skill provides guidance on performing structure and substructure searches using ChemQuery, SMILES strings, or InChI identifiers.

Is there a public API for HMDB access?

HMDB does not offer a public REST API. This skill facilitates access through web-based queries, R/Bioconductor packages like hmdbQuery, and instructions for processing bulk XML/SDF downloads.

What research workflows does this skill support?

It supports metabolite identification in untargeted metabolomics, biomarker discovery, pathway enrichment analysis, and general clinical chemistry research.

HMDB Database Explorer

Name: HMDB Database Explorer
Author: lifangda

bylifangda

•

Data Science & ML

Accesses the Human Metabolome Database to retrieve detailed chemical, clinical, and biological data for over 220,000 metabolites.

The HMDB Database skill empowers Claude to navigate and extract information from the world's most comprehensive resource for human small molecule metabolites. It enables researchers to perform structured searches for over 220,000 metabolites, retrieve detailed chemical properties, access clinical biomarker data, and interpret spectroscopic information (NMR/MS). By providing structured workflows for metabolite identification, pathway analysis, and data integration, this skill streamlines scientific research involving human metabolism, clinical chemistry, and drug discovery directly within the Claude environment.

Key Features

01Retrieve chemical properties including SMILES, InChI, and molecular weight

0216 GitHub stars

03Search 220,000+ metabolite entries by name, ID, or chemical structure

04Consult experimental and predicted spectroscopic data (NMR/MS) for identification

05Access clinical biomarker associations and normal/abnormal concentration ranges

06Map metabolites to biological pathways, reactions, and subcellular locations

Use Cases

01Researching clinical biomarkers and their specific associations with human diseases

02Identifying unknown metabolites in untargeted metabolomics studies using spectral matching

03Extracting metabolite datasets for integration into bioinformatics and data science pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add lifangda/claude-plugins hmdb-database

For use in Claude.ai and ChatGPT

Download Skill