alterlab-hmdb
Installation
SKILL.md
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.
Scripts
scripts/query_hmdb.py — fetch and parse an HMDB metabolite XML record by accession (stdlib only, JSON to stdout):
python scripts/query_hmdb.py HMDB0000001 # full accession
python scripts/query_hmdb.py 1 # bare number (zero-padded automatically)
Note: HMDB serves no public REST API. As of 2026-09 the whole site (including the .xml record URLs) sits behind a Cloudflare browser challenge, so scripted requests commonly get HTTP 403 — see "Programmatic Access" for the fallbacks. For bulk work download the XML/SDF dumps from https://www.hmdb.ca/downloads in a browser.