ensembl-database

name	ensembl-database
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.

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 LICENSE_NOTIFICATION.txt does not already exist in this skill 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

• Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.