Ensembl Database

What it does

Provides a structured interface and guidance for querying the Ensembl genome REST API. This skill outlines common operations such as retrieving gene, transcript and protein sequences, running Variant Effect Predictor (VEP) queries, finding orthologs/paralogs, and mapping coordinates between assemblies. It includes examples using a Python helper library and direct REST requests, plus scripts and reference docs included in the repo.

When to use it

Use when performing genomic data retrieval or analysis: gene annotation pipelines, variant consequence prediction, comparative genomics, retrieving sequences for downstream analysis, or converting coordinates between assemblies (GRCh37/GRCh38). Appropriate for researchers, bioinformaticians, and data pipelines that need programmatic access to Ensembl.

What's included

• Scripts: provided in the repository (e.g., ensembl_query.py) for common queries with rate-limiting and retry handling.
• References: an api_endpoints.md reference listing endpoints and parameters is present.
• Instructions: examples for Python (ensembl_rest) and direct REST usage, best-practice notes on rate limits and caching, workflow recipes for annotation and variant analysis.

Compatible agents

Best used with code-capable assistants that can run or generate Python scripts and API calls (Claude Code, Codex, Copilot).