Can I use this for non-human species?

Absolutely. It supports over 250 species, including common models like mouse, zebrafish, and fruit flies, using standard species identifiers.

Does this skill support the GRCh37 assembly?

Yes, it includes specific logic for assembly mapping and provides instructions for querying the GRCh37-specific REST server endpoints.

How are API rate limits handled?

The skill follows Ensembl's best practices by respecting the 15 requests per second limit and implementing retry logic for 429 status codes.

Do I need to install external packages?

While the REST API can be queried via standard HTTP libraries like 'requests', the 'ensembl_rest' Python package is recommended and supported for a more native experience.

Ensembl Genomic Database Integration

Name: Ensembl Genomic Database Integration
Author: jimmc414

byjimmc414

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324

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Data Science & ML

Accesses and queries the Ensembl REST API for genomic research, gene annotation, and variant analysis across 250+ species.

This skill provides a comprehensive interface for Claude to interact with the Ensembl genome database, a premier resource for vertebrate genomic data maintained by EMBL-EBI. It enables automated retrieval of gene annotations, DNA/protein sequences, and comparative genomics data, while supporting complex operations like Variant Effect Predictor (VEP) analysis and cross-assembly coordinate mapping. Ideal for bioinformaticians and researchers, it streamlines genomic data integration directly into computational workflows and discovery pipelines.

Key Features

01324 GitHub stars

02Query gene information by symbol or Ensembl ID across 250+ species

03Perform comparative genomics to find orthologs and paralogs

04Retrieve genomic, transcript (cDNA), and protein sequences in multiple formats

05Map genomic coordinates between different assembly versions (e.g., GRCh37 to GRCh38)

06Analyze genetic variants using the Variant Effect Predictor (VEP)

Use Cases

01Predicting the functional consequences of genetic variants in clinical research

02Automating gene annotation pipelines for large-scale genomic datasets

03Investigating evolutionary relationships through cross-species ortholog mapping

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos ensembl-database

For use in Claude.ai and ChatGPT

Download Skill