Agent skill · research science · google-deepmind
ensembl-database
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.
Why this skill is useful
Provides specific commands and workflows for querying the Ensembl database that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 5k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
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/ensembldatabaseLICENSE.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 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. Default Species: If the species is absent or ambiguous in the prompt, default to "human". You MUST explicitly flag this default to the user to ensure they are aware. Primary Transcripts: When listing transcripts for a gene, only return the MANE Select transcript (for human) or the Canonical transcript (for others) unless the user explicitly asks for all alternative isoforms. You MUST flag to the user when multiple transcripts are available and you are defaulting to the primary one. Assembly Handling: The default assembly is GRCh38. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/ensembl_database