Ensembl Database
Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic...
Install
npx skills add google-deepmind/science-skills --skill ensembl-database -g -a claude-code -y- Repository
- google-deepmind/science-skills3.4k
- Category
- Data and ML
- Updated
- 12d ago
- License
- Apache-2.0
- Context cost
- Mediumabout 2,110 tokens
- Runs scripts
- Yes, review before use
What it does
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
uv: Read theuvskill and follow its Setup instructions to ensureuvis 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:
- 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).
