Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ma-compbio-lab/SkillFoundry --skill ensembl-gene-lookupgit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/ensembl-gene-lookup)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/ensembl-gene-lookup"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/ensembl-gene-lookup/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/ensembl-gene-lookup"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/ensembl-gene-lookup.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00042 | $0.00463 |
| Opus 5 | $0.00021 | $0.00231 |
| Sonnet 5 | $0.00008 | $0.00093 |
| Haiku 4.5 | $0.00004 | $0.00046 |
Grade A, and why
ensembl-gene-lookup scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
Purpose
Resolve a gene symbol through Ensembl REST and return the corresponding gene lookup payload.
When to use
- You need a quick official Ensembl gene identifier lookup.
- You want lightweight gene metadata before a larger genomics workflow.
When not to use
- You need transcript-level or large-batch annotation.
- You need local-only execution.
Inputs
- Gene symbol
- Optional species and output path
Outputs
- JSON payload containing the xref candidates and the selected lookup record
Requirements
- Python 3.13+
- Network access to
rest.ensembl.org - Example asset fallback exists for the curated
BRCA1andBRCA2examples if the live API is temporarily unavailable.
Procedure
- Run
python3 skills/genomics/ensembl-gene-lookup/scripts/lookup_gene.py --symbol BRCA1 --out skills/genomics/ensembl-gene-lookup/assets/brca1_lookup.json. - Inspect
xrefsto confirm the chosen gene ID. - Use the
lookupblock for coordinates and display name.
Validation
- Command exits successfully.
- At least one xref is returned for a known symbol.
- Lookup block includes
id,display_name, and coordinates.
Failure modes and fixes
- No hits: confirm species and capitalization.
- Multiple matches: filter by
type == geneand inspect the candidates. - Official API timeout: rerun once; the curated BRCA example assets can still support deterministic example execution.
Safety and limits
- Metadata lookup only.
- Large-scale annotation should use more specialized batch tooling.
Examples
python3 .../lookup_gene.py --symbol TP53 --species homo_sapiens
Provenance
- Ensembl REST API: https://rest.ensembl.org/
- Ensembl lookup documentation: https://rest.ensembl.org/documentation/info/lookup
Related skills
scanpy-qc-starter
What ships with it
8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 57 lines · 42 tokens per session scan A c9dc1060c0fd
ensembl-gene-lookup is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (39 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 42 tokens to every session and 463 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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