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skill CX Codex GP ChatGPT official · OpenAI

hmdb-skill — Codex skill: search HMDB

A skill for searching metabolites, proteins, diseases, and pathways in the HMDB database. Submits compact requests and returns concise summaries.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill hmdb-skill -a codex
Open on GitHub

What hmdb-skill does

hmdb-skill uses scripts/rest_request.py for all HMDB queries. The unearth/q endpoint handles searches with query, category, and format=json parameters. Results are capped at 10 items via per_page=10 and max_items=10 to keep responses compact.

By default, the skill returns markdown summaries from the JSON response. If you need the full payload, set save_raw=true and the skill reports the file path. In long conversations, the skill resubmits requests instead of caching old results, ensuring fresh data from HMDB.

To install on Codex, run npx skills add openai/plugins --skill hmdb-skill; the skill then lives in .agents/skills/hmdb-skill/.

What it helps with

  • find a molecule or metabolite in HMDB by name
  • look up protein or enzyme information
  • search for a disease in the database
  • explore a biochemical pathway
  • get a concise search result summary

Example prompts for the agent

  • Find the structure of serotonin in HMDB
  • Show me pathways related to glycolysis in HMDB
  • Search HMDB for diabetes and give me a brief report

How to install hmdb-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill hmdb-skill -a codex

2Manually: put the files in place

.agents/skills/hmdb-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about hmdb-skill

How do I install hmdb-skill in Codex?

Run npx skills add openai/plugins --skill hmdb-skill. The skill installs to .agents/skills/hmdb-skill/SKILL.md.

What does hmdb-skill do?

It submits search queries to the HMDB database for metabolites, proteins, diseases, and pathways, returning compact markdown summaries. Each search is limited to 10 results.

How do I get the full response instead of a summary?

Set save_raw=true in the request parameters; the skill will save the full payload and report the file path.

See also

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