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skill CX Codex GP ChatGPT official · OpenAI

bgee-skill — Codex skill: what it does, how to install

This skill sends compact SPARQL requests to Bgee for healthy wild-type expression metadata and ontology-aware lookups. Use it when concise summaries are enough.

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

What bgee-skill does

bgee-skill lets Codex and ChatGPT query Bgee with compact SPARQL requests. It focuses on expression metadata from healthy wild-type samples and lookup patterns that use ontology terms. By default, the result is turned into a concise Markdown summary; raw output is returned only when requested.

All Bgee SPARQL work goes through scripts/sparql_request.py. The script reads one JSON object from stdin, with either query or query_path required. Optional fields control the response format, item and depth limits, timeout, and raw-output path. Start with small SELECT or ASK queries and add LIMIT early. Longer SPARQL documents can go through query_path.

Install it when an agent needs repeatable Bgee lookups and short answers. Choose another workflow for broad triple dumps or large raw exports.

What it helps with

  • query Bgee expression metadata
  • look up terms with ontology-aware patterns
  • turn SPARQL JSON into a short summary
  • save raw query results on request

Example prompts for the agent

  • Ask Bgee for a concise summary of healthy wild-type expression for this term.
  • Use an ontology-aware lookup and explain the returned metadata.
  • Run `scripts/sparql_request.py` with `query_path` and save the raw output.

How to install bgee-skill

1Skills CLI (Vercel)

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

2Manually: put the files in place

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

For all projects use ~/.agents/skills/

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Questions about bgee-skill

How do I install bgee-skill in Codex?

Run npx skills add openai/plugins --skill bgee-skill or npx skills add openai/plugins --skill bgee-skill -a codex. The skill file is placed at .agents/skills/bgee-skill/SKILL.md.

What does bgee-skill do?

It sends compact SPARQL requests to Bgee and returns concise summaries of healthy wild-type expression metadata. It also supports ontology-aware lookup patterns.

What input does bgee-skill require?

The script reads one JSON object from stdin and requires either query or query_path. Requests run through scripts/sparql_request.py with Python.

See also

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