ensembl-skill — Codex skill: what it does, how to install
Runs lightweight Ensembl REST API queries to deliver concise summaries of genes, genomic regions, and genetic variations.
npx skills add openai/plugins --skill ensembl-skill -a codexWhat ensembl-skill does
The skill talks to https://rest.ensembl.org through a bundled Python helper scripts/rest_request.py. Rather than flooding the context window with large JSON payloads, it converts biological records into short Markdown summaries. Raw JSON output is printed only when explicitly requested.
It focuses on standard Ensembl endpoints: identifier lookups (lookup/id/<id>), region overlaps (overlap/region/<species>/<region>), cross-references (xrefs/id/<id>), and variant records (variation/<species>/<id>). For region queries, the script limits output with max_items=10 to avoid context bloat.
Because the helper reads input parameters as JSON from standard input, Python must be available in the local environment. When complete uncompressed responses are needed, setting save_raw=true alongside raw_output_path dumps the payload directly to a file.
What it helps with
- fetch gene details by Ensembl identifier
- inspect genomic features overlapping a chromosomal region
- retrieve cross-references for a biological entity
- query variant annotations across species
Example prompts for the agent
- Look up gene ENSG00000141510 in Ensembl
- Find overlapping genes in region homo_sapiens 1:1000000-1002000
- Fetch cross-references for this Ensembl ID and summarize them
How to install ensembl-skill
1Skills CLI (Vercel)
npx skills add openai/plugins --skill ensembl-skill -a codex2Manually: put the files in place
.agents/skills/ensembl-skill/SKILL.mdFor all projects use ~/.agents/skills/
1Skills CLI (Vercel)
npx skills add openai/plugins --skill ensembl-skill -a claude-code2Manually: put the files in place
~/.claude/skills/ensembl-skill/SKILL.mdCopy the whole skill folder; for one project use .claude/skills/ensembl-skill/
Manually: put the files in place
.cursor/skills/ensembl-skill/SKILL.mdCursor also reads .agents/skills/ and .claude/skills/
1GitHub CLI
gh skill install openai/plugins ensembl-skill2Manually: put the files in place
.github/skills/ensembl-skill/SKILL.mdPlatform CLI
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/ensembl-skillManually: put the files in place
.devin/skills/ensembl-skill/SKILL.mdThe legacy .windsurf/skills/ path still works
Claude.ai
Zip the folder and upload it in Settings → Capabilities → Skills
Step by step, with commands for each platform: Codex skills: how to install, where they live, how to call them
Questions about ensembl-skill
How to install ensembl-skill in Codex?
Run npx skills add openai/plugins --skill ensembl-skill. To target the Codex environment explicitly, run npx skills add openai/plugins --skill ensembl-skill -a codex.
What does ensembl-skill do?
It queries the Ensembl REST API via a local Python script to fetch gene metadata, chromosome overlaps, and variants. By default, it condenses responses into readable Markdown summaries.
How do I get the full uncompressed API response?
Pass save_raw=true together with a destination file path in raw_output_path. This writes the original API payload directly to disk.
