Can I use this skill for clinical research?

Absolutely; it provides detailed clinical data, including biomarker associations and metabolite concentration ranges in various biological specimens like urine, serum, and CSF.

Does this skill provide access to NMR and MS spectra?

Yes, it includes guidance on accessing experimental and predicted NMR, MS, and MS-MS spectra for compound identification and spectral matching.

What is the primary use of the HMDB Database skill?

It is designed to help researchers search, identify, and analyze metabolites within the human body using the Human Metabolome Database (HMDB) version 5.0.

How does this skill handle programmatic access to the database?

It provides implementation patterns for using the hmdbQuery R package, as well as workflows for parsing bulk XML, SDF, and CSV datasets for local bioinformatics pipelines.

HMDB Scientific Database Access

Name: HMDB Scientific Database Access
Author: K-Dense-AI

byK-Dense-AI

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2,188

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Data Science & ML

Accesses the Human Metabolome Database (HMDB) to retrieve comprehensive data on small molecule metabolites, clinical biomarkers, and biochemical pathways.

This skill empowers Claude to act as a specialized assistant for metabolomics and clinical chemistry by providing direct guidance on utilizing the Human Metabolome Database (HMDB). It covers searching for over 220,000 metabolites by name, structure, or spectral data, while offering deep insights into chemical properties, disease associations, and metabolic pathways. Ideal for researchers and data scientists, it streamlines workflows for metabolite identification, biomarker discovery, and bioinformatic data integration by providing best practices for both web-based searches and programmatic data handling.

Key Features

01Retrieval of spectroscopic data for NMR and MS-based identification

02Guidance on metabolic pathway analysis and enzyme/transporter associations

03Access to clinical data including disease associations and concentration ranges

04Comprehensive metabolite search by name, HMDB ID, SMILES, or InChI

05Support for programmatic data access via R/Bioconductor and bulk dataset parsing

062,188 GitHub stars

Use Cases

01Mapping clinical biomarkers to specific metabolic pathways for disease research

02Automating the extraction of chemical properties for large-scale metabolomics datasets

03Identifying unknown metabolites in untargeted metabolomics studies using spectral matching

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills hmdb-database

For use in Claude.ai and ChatGPT

Download Skill