What species are supported by this Ensembl skill?

It supports over 250 vertebrate species, including humans (Homo sapiens), mice (Mus musculus), zebrafish (Danio rerio), and fruit flies (Drosophila melanogaster).

What kind of variant data can I retrieve?

You can look up variants by rsID or coordinates, predict functional consequences using VEP, access population frequency data, and retrieve phenotype associations.

Can I use this for GRCh37/hg19 coordinate mapping?

Yes, the skill includes logic to query the GRCh37-specific REST endpoint for legacy coordinate conversion and data retrieval alongside current GRCh38 assemblies.

How does the skill handle Ensembl API rate limits?

The skill implements best practices such as respecting the 15 requests per second limit, handling 429 status codes via Retry-After headers, and utilizing batch endpoints for bulk queries.

Ensembl Genome Database

Name: Ensembl Genome Database
Author: lifangda

bylifangda

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Data Science & ML

Queries the Ensembl REST API to retrieve genomic annotations, sequences, variants, and comparative genomics data for over 250 species.

This skill empowers Claude to interact directly with the Ensembl genome database, a premier resource for vertebrate genomics maintained by EMBL-EBI. It provides comprehensive tools for biological research, including gene lookups by symbol or ID, sequence extraction (DNA, protein, cDNA), variant effect prediction via VEP, and cross-species ortholog mapping. It is designed for bioinformaticians and researchers who need to automate genomic data retrieval, analyze genetic variations, or integrate multi-species comparative data into their research pipelines with built-in support for rate limiting and error handling.

Key Features

0116 GitHub stars

02Comprehensive gene lookups by symbol or Ensembl ID across 250+ species

03Comparative genomics tools for identifying orthologs and paralogs

04High-throughput sequence retrieval for DNA, transcripts, and proteins

05Assembly mapping for coordinate conversion between GRCh37 and GRCh38

06Variant Effect Predictor (VEP) integration for functional consequence analysis

Use Cases

01Predicting the functional impact of genetic variants in clinical or research samples

02Conducting evolutionary studies by comparing gene structures across multiple species

03Automating gene annotation and sequence retrieval for specific genomic regions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add lifangda/claude-plugins ensembl-database

For use in Claude.ai and ChatGPT

Download Skill