Individual skill

hmdb-database

Access the Human Metabolome Database (HMDB) to search metabolites by name/structure/ID and extract chemical/biological/clinical fields when you need metabolomics research data or automated HMDB XML mining.

scientific-skills/Evidence Insight/hmdb-database/SKILL.md

Read pinned source

Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91

What was checked

Matches the observed repository HEAD: Yes
Scanner rules are current: Yes
Repository scan complete: No
Skill scan complete: No
Observed behavior: Network or broad shell
Last checked: Nov 9, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings): 2,042
Repository last updated: Sep 17, 2026
License: MIT

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

bioinformatics Repository topic
computational-biology Repository topic
data-analysis Repository topic
ai Repository topic
biology Repository topic
cancer-genomics Repository topic
data-visualization Repository topic
differential-expression Repository topic
genomics Repository topic
medical Repository topic
data Derived category
research Derived category
data-databases Derived category

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files

SKILL.mdcore · 3,943 bytes
SKILL.mdcore · 3,943 bytes
hmdb-database_audit_result_v1.jsonasset · 11,705 bytes
references/hmdb_data_fields.mddoc · 1,245 bytes
scripts/hmdb_parser.pyruns · 2,534 bytes

Read excerpt

> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You need to look up a metabolite by **common name** (e.g., “Caffeine”) and retrieve its HMDB entry data.
- You have an **HMDB ID** (e.g., `HMDB0000001`) and want to extract standardized chemical/biological/clinical fields for downstream analysis.
- You want to build a **local, scriptable pipeline** to mine the HMDB XML dump instead of manually browsing the website.
- You need to **map HMDB identifiers** to external resources (e.g., KEGG, PubChem, ChEBI) for integration tasks.
- You are preparing metabolomics datasets and need **pathway/enzyme/transporter** annotations from HMDB entries.

## Key Features

- Search metabolites by:
  - Text name
  - HMDB identifier (e.g., `HMDB0000001`)