ensembl-database

1# Ensembl Database: ID Mapping and Genomic Features
2 
3## Prerequisites
4 
51.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
6    `uv` is installed and on PATH.
72.  **User Notification**: If .licenses/ensembl_database_LICENSE.txt does not
8    already exist in the workspace root directory then (1) prominently notify
9    the user to check the terms at https://useast.ensembl.org/index.html and
10    https://github.com/Ensembl/ensembl-rest/wiki, then (2) create the file
11    recording the notification text and timestamp.
12 
13## Overview
14 
15The Ensembl database is a resource for genome annotation. This skill allows you
16to interact with the Ensembl REST API to resolve ambiguous symbols,
17cross-reference IDs (RefSeq, HGNC, UniProt, ENSG), fetch raw sequences, and
18retrieve detailed transcript structures.
19 
20**Key Concepts:**
21 
22-   **ENSG (Gene):** Stable identifier for a human gene. Other species will have
23    different three-letter species codes.
24-   **ENST (Transcript):** Stable identifier for a transcript (splicing
25    isoform).
26-   **ENSP (Protein):** Stable identifier for a translated protein.
27-   **MANE Select:** The consensus primary transcript agreed upon by Ensembl and
28    NCBI.
29-   **Canonical:** Ensembl's representative transcript (used if MANE is not
30    available or non-human).
31 
32## Core Rules
33 
34-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
35    database rather than accessing the database directly. The scripts
36…