Ensembl Database

If you're working with genomic data and tired of manually looking up gene identifiers across different databases, this handles the tedious ID mapping between RefSeq, HGNC, UniProt, and Ensembl formats through their REST API. It also pulls raw sequences and transcript structures when you need them. Built by Google DeepMind as part of their science-skills collection, which explains the 2.4K stars. The license notification requirement is a nice touch, making sure you're aware of Ensembl's terms before hitting their API. Most useful when you're dealing with cross-referenced genomic datasets and need to normalize identifiers without leaving your workflow.

skills.sh installs: 2.3K
GitHub stars: 3.4K
last updated: Aug 21, 2026

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Install

$ npx -y skills add google-deepmind/science-skills --skill ensembl-database --agent claude-code

Installs into .claude/skills of the current project.

Files

Ensembl Database: ID Mapping and Genomic Features

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
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:

SKILL.md on GitHub