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 GPTomics/bioSkills --skill ensembl-restgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/ensembl-rest)<a href="https://agentmods.dev/skills/gptomics/bioskills/ensembl-rest"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/ensembl-rest/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/gptomics/bioskills/ensembl-rest"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/ensembl-rest.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 | $0.00143 | $0.03931 |
| Opus 5 | $0.00072 | $0.01965 |
| Sonnet 5 | $0.00029 | $0.00786 |
| Haiku 4.5 | $0.00014 | $0.00393 |
Grade A, and why
bio-ensembl-rest scanned grade A with 1 finding 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 8d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
- Python: `requests.get('https://rest.ensembl.org/...')` Copies of this mod
1 near-identical copy found in the catalogue:
- bio-ensembl-rest — 98% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 334 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: requests 2.31+, Ensembl REST API (release 110+); Ensembl release schedule is roughly quarterly
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show requests - API surface: check release notes at https://rest.ensembl.org
Each Ensembl release has an archive REST endpoint (e.g. https://e110.rest.ensembl.org) for reproducibility.
Ensembl REST
"Pull Ensembl-native gene / transcript / variant data programmatically" -> Ensembl REST is distinct from NCBI Entrez and BioMart. It is the right answer for: stable Ensembl IDs, transcript / exon structure, VEP (Variant Effect Predictor) annotation, Compara orthologs at vertebrate scale, regulatory feature annotation, and any workflow rooted in Ensembl's coordinate system.
Two facts dominate Ensembl REST work: (1) the 15 req/sec / 55,000 req/hour rate limit — high enough for hundreds of queries, low enough that bulk work (>5,000) belongs in BioMart instead; (2) versioned archive endpoints — https://e110.rest.ensembl.org pins to release 110 for reproducibility, while https://rest.ensembl.org follows the current release.
- Python:
requests.get('https://rest.ensembl.org/...') - Web: https://rest.ensembl.org (interactive doc with try-it-now)
- R:
biomaRtfor bulk (seebiomart-queries); REST viahttr
Required Setup
import requests
import time
BASE = 'https://rest.ensembl.org'
HEADERS = {'Accept': 'application/json'}
SLEEP = 0.07 # 15 req/sec ceiling
No API key required. Respect Retry-After header on 429.
Ensembl divisions
Ensembl is divided by clade. Different REST hosts:
| Division | Host | Scope |
|---|---|---|
| Vertebrates | https://rest.ensembl.org | Human, mouse, fish, etc. (the "main" Ensembl) |
| Plants | https://rest.ensembl.org (plants division also accessible) | Arabidopsis, rice, etc. via Ensembl Genomes |
| Fungi | https://rest.ensemblgenomes.org | Yeasts, Aspergillus, etc. |
| Metazoa | https://rest.ensemblgenomes.org | Insects, nematodes, etc. |
| Bacteria | https://rest.ensemblgenomes.org | Limited (most bacteria in NCBI) |
What ships with it
4 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.
- 8d ago First seen · 334 lines · 143 tokens per session scan A e610af8e7336
bio-ensembl-rest is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 143 tokens to every session and 3,931 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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