Agent skill · research science · aiskillstore
hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
Why this skill is useful
Provides access to niche metabolomics data and specific querying capabilities that the AI wouldn't reliably generate on its own.
What it needs
About 5k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
HMDB Database Overview The Human Metabolome Database (HMDB) is a comprehensive, freely available resource containing detailed information about small molecule metabolites found in the human body. When to Use This Skill This skill should be used when performing metabolomics research, clinical chemistry, biomarker discovery, or metabolite identification tasks. Database Contents HMDB version 5.0 (current as of 2025) contains: 220,945 metabolite entries covering both water-soluble and lipid-soluble compounds 8,610 protein sequences for enzymes and transporters involved in metabolism 130+ data fields per metabolite including: Chemical properties (structure, formula, molecular weight, InChI, SMILES) Clinical data (biomarker associations, diseases, normal/abnormal concentrations) Biological information (pathways, reactions, locations) Spectroscopic data (NMR, MS, MS-MS spectra) External database links (KEGG, PubChem, MetaCyc, ChEBI, PDB, UniProt, GenBank) Core Capabilities 1. Web-Based Metabolite Searches Access HMDB through the web interface at https://www.hmdb.ca/ for: Text Searches: Search by metabolite name, synonym, or identifier (HMDB ID) Example HMDB IDs: HMDB0000001, HMDB0001234 Search by disease associations or pathway involvement Query by biological specimen type (urine, serum, CSF, saliva, feces, sweat) Structure-Based Searches: Use ChemQuery for structure and substructure searches Search by molecular weight or molecular weight range Use SMILES or InChI strings to find compounds Spectral Searches: LC-MS spectral matching GC-MS spectral matching NMR spectral searches for metabolite identification Advanced Searches: Combine multiple criteria (name, properties, concentration ranges) Filter by biological locations or specimen types Search by protein/enzyme associations 2. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/hmdb-database--77de8a