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Agent skill

Ensembl Database

by aipoch in aipoch/medical-research-skills

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

MITAuto-check passedResearch & Science

Install Ensembl Database

skills CLI
$ npx skills add aipoch/medical-research-skills --skill ensembl-database -a claude-code

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

GitHub CLI
$ gh skill install aipoch/medical-research-skills ensembl-database --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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/ensembl-database' .claude/skills/ensembl-database && 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/

Facts

Skill name
ensembl-database
GitHub stars
2k
Token cost
~1.5k tokens
SKILL.md length
626 words
Files
4 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

  • Works in 5 steps: When to Use → Key Features → Dependencies → …
  • You need gene/ID lookups
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 6 more sections
  • Runs Python scripts from its folder; calls python; reaches rest.ensembl.org

What it does

Ensembl Database is an agent skill from aipoch/medical-research-skills. Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `ensembl-database_audit_result_v1.json`, `references/api_endpoints.md` and `scripts/query_ensembl.py`).

It sits in Research & Science, covering Bioinformatics and REST APIs. It works with Ensembl. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need gene/ID lookups
  • Sequence retrieval
  • Variant effect prediction (VEP)
  • Homology/assembly coordinate mapping

Example prompts

  • “/ensembl-database”

Requirements

  • Python 3

Workflow steps

5 steps, taken from the step headings in SKILL.md.

  1. When to Use
  2. Key Features
  3. Dependencies
  4. Example Usage
  5. Implementation Details

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. 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

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    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

    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 Database loads about 1.5k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 50 tokens; SKILL.md has 626 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~50
When it runs · the whole SKILL.md, loaded when a task matches
~1.5k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~1.6k

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); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 626 words, ~1,477 tokens.

Download SKILL.mdSave it as .claude/skills/ensembl-database/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.
name
ensembl-database
description
Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

Ensembl Database Skill

When to Use

  • Use this skill when you need access ensembl rest api for vertebrate genomic data; use when you need gene/id lookups, sequence retrieval, variant effect prediction (vep), or homology/assembly coordinate mapping in a reproducible workflow.
  • Use this skill when a evidence insight task needs a packaged method instead of ad-hoc freeform output.
  • Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
  • Use this skill when scripts/query_ensembl.py is the most direct path to complete the request.
  • Use this skill when you need the ensembl-database package behavior rather than a generic answer.

Key Features

  • Scope-focused workflow aligned to: Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.
  • Packaged executable path(s): scripts/query_ensembl.py.
  • Reference material available in references/ for task-specific guidance.
  • Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

  • Python: 3.10+. Repository baseline for current packaged skills.
  • Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

bash
cd "20260316/scientific-skills/Evidence Insight/ensembl-database"
python -m py_compile scripts/query_ensembl.py
python scripts/query_ensembl.py --help

Example run plan:

  1. Confirm the user input, output path, and any required config values.
  2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
  3. Run python scripts/query_ensembl.py with the validated inputs.
  4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

  • Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
  • Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
  • Primary implementation surface: scripts/query_ensembl.py.
  • Reference guidance: references/ contains supporting rules, prompts, or checklists.
  • Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
  • Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

1. When to Use

  • Gene-centric queries: When you need to resolve a gene symbol or region to Ensembl identifiers and basic annotations (e.g., BRCA2 in human).
  • Sequence extraction: When you need DNA/cDNA/protein sequences for a known Ensembl gene/transcript/protein ID in FASTA or JSON.
  • Variant interpretation: When you need to predict functional consequences of variants using VEP from HGVS notation.
  • Comparative genomics: When you need ortholog/paralog relationships across vertebrate species.
  • Assembly/coordinate mapping: When you need to map coordinates between assemblies (e.g., GRCh37 ↔ GRCh38).
Show full SKILL.md (232 more words)Show less

2. Key Features

  • Query Ensembl REST endpoints for:
    • Gene lookup by symbol, Ensembl ID, or genomic region
    • Sequence retrieval (DNA, cDNA, protein) in FASTA/JSON
    • Variant Effect Predictor (VEP) analysis from HGVS inputs
    • Homology retrieval (orthologs/paralogs)
    • Assembly/coordinate mapping between common human assemblies
  • CLI helper script for repeatable queries:
    • scripts/query_ensembl.py (wrapper around an ensembl_rest client)
  • Reference documentation for endpoints:

3. Dependencies

  • Python >=3.8
  • ensembl_rest (Python client; version depends on your environment)
  • Network access to https://rest.ensembl.org

4. Example Usage

CLI: Gene lookup by symbol
bash
python scripts/query_ensembl.py --action lookup --species human --symbol BRCA2
CLI: Retrieve sequence by Ensembl ID
bash
python scripts/query_ensembl.py --action sequence --id ENSG00000139618
CLI: Variant effect prediction (VEP) by HGVS
bash
python scripts/query_ensembl.py --action vep --species human --hgvs "ENST00000380152.8:c.68_69delAG"

5. Implementation Details

Script entry point
  • Tool: scripts/query_ensembl.py
  • Purpose: Provide a simple command-line interface that dispatches to Ensembl REST calls via an ensembl_rest client.
Core parameters
  • --action: Operation selector.
    • Supported values: lookup, sequence, vep
  • --species: Target species name used by Ensembl REST (e.g., human).
  • --symbol: Gene symbol used for lookup actions (e.g., BRCA2).
  • --id: Ensembl stable ID used for sequence retrieval (e.g., ENSG..., ENST..., ENSP...).
  • --hgvs: HGVS notation string used for VEP (e.g., ENST...:c.123A>G).
Data types and outputs
  • Lookup: Returns gene/transcript metadata as provided by Ensembl REST.
  • Sequence: Returns DNA/cDNA/protein sequence; format depends on the endpoint/options (commonly FASTA or JSON).
  • VEP: Returns consequence annotations and (when available) population frequency fields as provided by Ensembl VEP REST responses.
Endpoint reference

For the exact REST paths, required parameters, and response schemas, see:

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files (scripts, references) in scientific-skills/Evidence Insight/ensembl-database of aipoch/medical-research-skills.

  • SKILL.md
  • ensembl-database_audit_result_v1.json
  • references/api_endpoints.md
  • scripts/query_ensembl.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Ensembl Database 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 Database compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Ensembl Database this skillaipoch/medical-research-skills2k—~1.5kAutomated safety check: PassMIT
Bio Ensembl RESTGPTomics/bioSkills1.2k2 repos~3.6kAutomated safety check: PassMIT
Snpeff Variant Annotationjaechang-hits/SciAgent-Skills3701 repos~5.4kAutomated safety check: PassMIT
Mouse Phenome Databasejaechang-hits/SciAgent-Skills3701 repos~6.8kAutomated safety check: PassCC-BY-4.0
Ensembl Databasejaechang-hits/SciAgent-Skills3701 repos~4kAutomated safety check: PassApache-2.0
Uniprot Protein Databasejaechang-hits/SciAgent-Skills3701 repos~3.4kAutomated safety check: PassCC-BY-4.0

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Works with

Categories

Questions about Ensembl Database

What does Ensembl Database do?

Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping. Ensembl Database is an agent skill from aipoch/medical-research-skills. Access Ensembl REST API for vertebrate genomic data; use when you need gene/ID lookups, sequence retrieval, variant effect prediction (VEP), or homology/assembly coordinate mapping.

When should I use Ensembl Database?

Ensembl Database fits situations like: you need gene/ID lookups; sequence retrieval; variant effect prediction (VEP); homology/assembly coordinate mapping.

How do I install Ensembl Database in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill ensembl-database -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/ensembl-database in aipoch/medical-research-skills) into .claude/skills/ensembl-database in your project. Claude Code loads it when a task matches its description.

How do I install Ensembl Database in Codex?

Run `npx skills add aipoch/medical-research-skills --skill ensembl-database -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/ensembl-database in aipoch/medical-research-skills) into .agents/skills/ensembl-database in your project. Codex loads it when a task matches its description.

Can I use Ensembl Database 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 aipoch/medical-research-skills --skill ensembl-database -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-database, .gemini/skills/ensembl-database, .github/skills/ensembl-database and .opencode/skills/ensembl-database in your project.

What does Ensembl Database need to run?

Going by SKILL.md and its folder, Ensembl Database needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Ensembl Database access the network?

SKILL.md names 1 domain. In commands or code: rest.ensembl.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Ensembl Database 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Ensembl Database use?

Ensembl Database is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Ensembl Database use?

About 1.5k tokens (SKILL.md is roughly 5.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 114 tokens, read only when the agent opens those files.

What are the alternatives to Ensembl Database?

Skills that share tags, products or a category with Ensembl Database: Bio Ensembl REST (GPTomics/bioSkills, 1.2k stars), Snpeff Variant Annotation (jaechang-hits/SciAgent-Skills, 370 stars), Mouse Phenome Database (jaechang-hits/SciAgent-Skills, 370 stars) and Ensembl Database (jaechang-hits/SciAgent-Skills, 370 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Ensembl Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

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