Agent skill

Ensembl REST API

by wentorai in wentorai/research-plugins

Query gene, sequence, and variant data via the Ensembl REST API

Install Ensembl REST API

skills CLI

$ npx skills add wentorai/research-plugins --skill ensembl-rest-api -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins ensembl-rest-api --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/biomedical/ensembl-rest-api .claude/skills/ensembl-rest-api && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "ensembl-rest-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api into .claude/skills/ensembl-rest-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ensembl-rest-api", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add wentorai/research-plugins --skill ensembl-rest-api -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins ensembl-rest-api --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/domains/biomedical/ensembl-rest-api .agents/skills/ensembl-rest-api && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "ensembl-rest-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api into .agents/skills/ensembl-rest-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ensembl-rest-api", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wentorai/research-plugins --skill ensembl-rest-api -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins ensembl-rest-api --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/domains/biomedical/ensembl-rest-api .cursor/skills/ensembl-rest-api && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "ensembl-rest-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api into .cursor/skills/ensembl-rest-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ensembl-rest-api", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/domains/biomedical/ensembl-rest-api

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add wentorai/research-plugins --skill ensembl-rest-api -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins ensembl-rest-api --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/domains/biomedical/ensembl-rest-api .gemini/skills/ensembl-rest-api && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "ensembl-rest-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api into .gemini/skills/ensembl-rest-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ensembl-rest-api", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install wentorai/research-plugins ensembl-rest-api

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add wentorai/research-plugins --skill ensembl-rest-api -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/domains/biomedical/ensembl-rest-api .github/skills/ensembl-rest-api && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "ensembl-rest-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api into .github/skills/ensembl-rest-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ensembl-rest-api", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add wentorai/research-plugins --skill ensembl-rest-api -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install wentorai/research-plugins ensembl-rest-api --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/domains/biomedical/ensembl-rest-api .opencode/skills/ensembl-rest-api && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "ensembl-rest-api" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/domains/biomedical/ensembl-rest-api into .opencode/skills/ensembl-rest-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "ensembl-rest-api", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: ensembl-rest-api
GitHub stars: 298
Used in: 1 other repo
Token cost: ~2k tokens
SKILL.md length: 472 words
Files: 1
Skills in repo: 405
Repo updated: Jun 19, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Query gene, sequence, and variant data via the Ensembl REST API

Tasks that involve REST APIs
SKILL.md covers Overview, Authentication, Core Endpoints and Rate Limits, plus 3 more sections
Calls curl; reaches rest.ensembl.org and grch37.rest.ensembl.org
Tasks that involve Bioinformatics

What it does

Ensembl REST API is an agent skill from wentorai/research-plugins. Query gene, sequence, and variant data via the Ensembl REST API

Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Backend & APIs, covering REST APIs and Bioinformatics. It works with Ensembl. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.

When your agent uses it

Tasks that involve REST APIs
Tasks that involve Bioinformatics

Example prompts

“/ensembl-rest-api”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- curl
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
- rest.ensembl.org
- grch37.rest.ensembl.org
Also links to:
- ensembl.org
- pachterlab.github.io
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Ensembl REST API loads about 2k tokens when it runs. Until then it costs about 20 tokens; SKILL.md has 472 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~20
When it runs · the whole SKILL.md, loaded when a task matches: ~2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 472 words, ~1,991 tokens.

Download SKILL.mdSave it as .claude/skills/ensembl-rest-api/SKILL.md (or your agent's skills folder).

name: ensembl-rest-api
description: Query gene, sequence, and variant data via the Ensembl REST API

Ensembl REST API Guide

Overview

Ensembl is a genome browser and annotation system maintained by EMBL-EBI and the Wellcome Sanger Institute, providing reference assemblies, gene annotations, variant data, and comparative genomics for over 300 vertebrate genomes. It is the genomic reference underpinning gget, PyEnsembl, and BioMart.

The REST API exposes Ensembl data via stateless HTTP. Researchers can look up genes by symbol or stable ID, retrieve genomic/cDNA/protein sequences, query variant annotations (rsIDs, clinical significance, consequences), access cross-references (HGNC, UniProt, RefSeq, OMIM), and obtain assembly metadata. Responses in JSON or XML.

Authentication

No authentication required. All endpoints are publicly accessible. Users needing higher throughput can register for an API token.

Core Endpoints

lookup/symbol: Gene Lookup by Symbol

Retrieve gene metadata: coordinates, biotype, canonical transcript.

URL: GET https://rest.ensembl.org/lookup/symbol/{species}/{symbol}
Parameters:

Parameter	Type	Required	Description
species	string	Yes	Species name (e.g., `homo_sapiens`)
symbol	string	Yes	Gene symbol (e.g., `BRCA1`, `TP53`)
expand	int	No	Set to 1 to include transcripts and translations
content-type	string	Yes	`application/json` or `text/xml`

Example:

bash

curl "https://rest.ensembl.org/lookup/symbol/homo_sapiens/BRCA1?content-type=application/json"

Response (actual):

json

{
  "display_name": "BRCA1",
  "description": "BRCA1 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1100]",
  "object_type": "Gene", "species": "homo_sapiens",
  "assembly_name": "GRCh38", "biotype": "protein_coding",
  "seq_region_name": "17", "start": 43044292, "end": 43170245, "strand": -1,
  "id": "ENSG00000012048", "canonical_transcript": "ENST00000357654.9"
}

sequence/id: Sequence Retrieval

Retrieve genomic, cDNA, CDS, or protein sequences by Ensembl stable ID.

URL: GET https://rest.ensembl.org/sequence/id/{id}
Parameters:

Parameter	Type	Required	Description
id	string	Yes	Ensembl stable ID (e.g., `ENSG00000012048`)
type	string	No	`genomic`, `cdna`, `cds`, or `protein`
expand_5prime	int	No	Expand 5' flanking region by N bases
expand_3prime	int	No	Expand 3' flanking region by N bases
content-type	string	Yes	`application/json` or `text/plain` (FASTA)

Example:

bash

curl "https://rest.ensembl.org/sequence/id/ENSG00000012048?content-type=application/json&type=genomic"

Response (actual, seq truncated):

json

{
  "id": "ENSG00000012048", "query": "ENSG00000012048",
  "desc": "chromosome:GRCh38:17:43044292:43170245:-1",
  "molecule": "DNA",
  "seq": "AAAGCGTGGGAATTACAGATAAATTAAAACTGTGGAACCCCTTTCCTCGGCTGCCGCCAAGGTGTTCGG..."
}

xrefs/symbol: Cross-References

Map a gene symbol to Ensembl stable IDs and external database identifiers.

URL: GET https://rest.ensembl.org/xrefs/symbol/{species}/{symbol}
Key params: species (required), symbol (required), external_db (optional filter, e.g., UniProt)
Example:

bash

curl "https://rest.ensembl.org/xrefs/symbol/homo_sapiens/TP53?content-type=application/json"

Response (actual): [{"type":"gene","id":"ENSG00000141510"},{"type":"gene","id":"LRG_321"}]

Use xrefs/id/{id} to expand an Ensembl ID to all external cross-references (UniProt, HGNC, RefSeq, OMIM).

Show full SKILL.md (189 more words)Show less

variation: Variant Annotation

Retrieve variant data by rsID: mappings, alleles, consequence, clinical significance.

URL: GET https://rest.ensembl.org/variation/{species}/{id}
Key params: species (required), id (required, e.g., rs699)
Example:

bash

curl "https://rest.ensembl.org/variation/homo_sapiens/rs699?content-type=application/json"

Response (actual, synonyms truncated):

json

{
  "name": "rs699", "var_class": "SNP",
  "most_severe_consequence": "missense_variant",
  "clinical_significance": ["benign"],
  "evidence": ["Frequency","1000Genomes","Cited","ESP","Phenotype_or_Disease","ExAC","TOPMed","gnomAD"],
  "mappings": [{"location":"1:230710048-230710048","allele_string":"A/G","strand":1,"assembly_name":"GRCh38"}]
}

info/assembly: Assembly Metadata

URL: GET https://rest.ensembl.org/info/assembly/{species}
Response (actual): Returns assembly_name ("GRCh38.p14"), assembly_date ("2013-12"), assembly_accession ("GCA_000001405.29"), full karyotype array (1-22, X, Y, MT), and 347 top_level_region entries.

Rate Limits

Without token: 15 requests per second per IP.
With token: higher limits available upon registration.
Response headers: X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Reset on every response.
Batch POST endpoints (/lookup/id, /sequence/id): accept up to 1000 IDs per request.
GRCh37 mirror: https://grch37.rest.ensembl.org

Academic Use Cases

Gene annotation: Look up coordinates and biotypes for HGNC symbols to annotate RNA-seq results.
Variant interpretation: Retrieve consequence types and clinical significance for GWAS rsIDs.
ID mapping: Map between Ensembl, UniProt, RefSeq, and HGNC identifiers.
Primer design: Fetch genomic sequences with flanking regions for PCR or CRISPR targeting.
Comparative genomics: Query homology endpoints for orthologs across species.

Code Examples (Python)

Gene Lookup and Sequence Retrieval

python

import requests

BASE = "https://rest.ensembl.org"
HEADERS = {"Content-Type": "application/json"}

gene = requests.get(f"{BASE}/lookup/symbol/homo_sapiens/BRCA1", headers=HEADERS).json()
print(f"{gene['display_name']} ({gene['id']}) chr{gene['seq_region_name']}:{gene['start']}-{gene['end']}")

seq = requests.get(f"{BASE}/sequence/id/{gene['id']}?type=cds", headers=HEADERS).json()
print(f"CDS length: {len(seq['seq'])} bp")

Batch ID Lookup (POST)

python

import requests

ids = ["ENSG00000012048", "ENSG00000141510", "ENSG00000157764"]  # BRCA1, TP53, BRAF
resp = requests.post(
    "https://rest.ensembl.org/lookup/id",
    headers={"Content-Type": "application/json", "Accept": "application/json"},
    json={"ids": ids}
)
for ens_id, info in resp.json().items():
    print(f"{info['display_name']:10s} chr{info['seq_region_name']}:{info['start']}-{info['end']}")

Variant Annotation Pipeline

python

import requests

for rsid in ["rs699", "rs1042522", "rs334"]:
    v = requests.get(
        f"https://rest.ensembl.org/variation/homo_sapiens/{rsid}",
        headers={"Content-Type": "application/json"}
    ).json()
    loc = v["mappings"][0]["location"] if v.get("mappings") else "N/A"
    print(f"{v['name']:12s} {v['var_class']:5s} {v['most_severe_consequence']:25s} {loc}")

References

REST API docs: https://rest.ensembl.org/documentation
Ensembl browser: https://www.ensembl.org
gget toolkit (built on Ensembl REST): https://pachterlab.github.io/gget/
GRCh37 archive API: https://grch37.rest.ensembl.org

Files

Just SKILL.md in skills/domains/biomedical/ensembl-rest-api of wentorai/research-plugins.

Open the folder on GitHubat commit bf44b3c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.

brycewang-stanford/Auto-Empirical-Research-Skillsskills/43-wentorai-research-plugins/skills/domains/biomedical/ensembl-rest-api

Compare with similar skills

Ensembl REST API next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Ensembl REST API compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Ensembl REST API this skillwentorai/research-plugins	298	1 repos	~2k	Automated safety check: Pass	MIT	3 mo ago
Snpeff Variant Annotationjaechang-hits/SciAgent-Skills	371	1 repos	~5.4k	Automated safety check: Pass	MIT	10 days ago
Bio Ensembl RESTGPTomics/bioSkills	1.2k	2 repos	~3.6k	Automated safety check: Pass	MIT	1 mo ago
Ensembl Databaseaipoch/medical-research-skills	2k	—	~1.5k	Automated safety check: Pass	MIT	22 days ago
Mouse Phenome Databasejaechang-hits/SciAgent-Skills	371	1 repos	~6.8k	Automated safety check: Pass	CC-BY-4.0	10 days ago
Encode Ccres Databasegoogle-deepmind/science-skills	3.2k	1 repos	~1.7k	Automated safety check: Pass	Apache-2.0	24 days ago

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Questions about Ensembl REST API

What does Ensembl REST API do?

Query gene, sequence, and variant data via the Ensembl REST API. Ensembl REST API is an agent skill from wentorai/research-plugins.

When should I use Ensembl REST API?

Ensembl REST API fits situations like: tasks that involve REST APIs; tasks that involve Bioinformatics.

How do I install Ensembl REST API in Claude Code?

Run `npx skills add wentorai/research-plugins --skill ensembl-rest-api -a claude-code`. Or copy the skill folder (skills/domains/biomedical/ensembl-rest-api in wentorai/research-plugins) into .claude/skills/ensembl-rest-api in your project. Claude Code loads it when a task matches its description.

How do I install Ensembl REST API in Codex?

Run `npx skills add wentorai/research-plugins --skill ensembl-rest-api -a codex`. Or copy the skill folder (skills/domains/biomedical/ensembl-rest-api in wentorai/research-plugins) into .agents/skills/ensembl-rest-api in your project. Codex loads it when a task matches its description.

Can I use Ensembl REST API in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill ensembl-rest-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/ensembl-rest-api, .gemini/skills/ensembl-rest-api, .github/skills/ensembl-rest-api and .opencode/skills/ensembl-rest-api in your project.

What does Ensembl REST API need to run?

Going by SKILL.md and its folder, Ensembl REST API needs the command-line tools its instructions call (curl). Our summary lists: Python 3.

Does Ensembl REST API access the network?

SKILL.md names 4 domains. In commands or code: rest.ensembl.org and grch37.rest.ensembl.org; the agent is likely to contact these when it follows the instructions. As links in the text: ensembl.org and pachterlab.github.io. This is read from the text; nothing was executed.

Is Ensembl REST API safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Ensembl REST API use?

Ensembl REST API is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Ensembl REST API use?

About 2k tokens (SKILL.md is roughly 8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Ensembl REST API?

Skills that share tags, products or a category with Ensembl REST API: Snpeff Variant Annotation (jaechang-hits/SciAgent-Skills, 371 stars), Bio Ensembl REST (GPTomics/bioSkills, 1.2k stars), Ensembl Database (aipoch/medical-research-skills, 2k stars) and Mouse Phenome Database (jaechang-hits/SciAgent-Skills, 371 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Ensembl REST API?

wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.

Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Ensembl REST API

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Ensembl REST API Guide

Overview

Authentication

Core Endpoints

lookup/symbol: Gene Lookup by Symbol

sequence/id: Sequence Retrieval

xrefs/symbol: Cross-References

variation: Variant Annotation

info/assembly: Assembly Metadata

Rate Limits

Academic Use Cases

Code Examples (Python)

Gene Lookup and Sequence Retrieval

Batch ID Lookup (POST)

Variant Annotation Pipeline

References

Files

Used in 1 other repository

Compare with similar skills

Similar skills

More from wentorai/research-plugins

Related

Questions about Ensembl REST API