# Ensembl Database

Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Data and ML
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill ensembl-database -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill ensembl-database -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill ensembl-database -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill ensembl-database -g -a gemini-cli -y`

## Description

Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP). Use this skill as a primary ID translator, genomic sequence database and variant effect prediction tool.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Ensembl Database: ID Mapping and Genomic Features

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/ensembl_database_LICENSE.txt does not
    already exist in the workspace root directory then (1) prominently notify
    the user to check the terms at https://useast.ensembl.org/index.html and
    https://github.com/Ensembl/ensembl-rest/wiki, then (2) create the file
    recording the notification text and timestamp.

## Overview

The Ensembl database is a resource for genome annotation. This skill allows you
to interact with the Ensembl REST API to resolve ambiguous symbols,
cross-reference IDs (RefSeq, HGNC, UniProt, ENSG), fetch raw sequences, and
retrieve detailed transcript structures.

**Key Concepts:**

-   **ENSG (Gene):** Stable identifier for a human gene. Other species will have
    different three-letter species codes.
-   **ENST (Transcript):** Stable identifier for a transcript (splicing
    isoform).
-   **ENSP (Protein):** Stable identifier for a translated protein.
-   **MANE Select:** The consensus primary transcript agreed upon by Ensembl and
    NCBI.
-   **Canonical:** Ensembl's representative transcript (used if MANE is not
    available or non-human).

## Core Rules

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/ensembl_database/SKILL.md