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 and may rate-limit/block automated fetches; for bulk work download the XML/SDF dumps from https://www.hmdb.ca/downloads.

When to Use This Skill