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

Data Science & ML

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

About

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

324 GitHub stars
Query gene information by symbol or Ensembl ID across 250+ species
Perform comparative genomics to find orthologs and paralogs
Retrieve genomic, transcript (cDNA), and protein sequences in multiple formats
Map genomic coordinates between different assembly versions (e.g., GRCh37 to GRCh38)
Analyze genetic variants using the Variant Effect Predictor (VEP)

Use Cases

Predicting the functional consequences of genetic variants in clinical research
Automating gene annotation pipelines for large-scale genomic datasets
Investigating evolutionary relationships through cross-species ortholog mapping

About

Key Features

324 GitHub stars
Query gene information by symbol or Ensembl ID across 250+ species
Perform comparative genomics to find orthologs and paralogs
Retrieve genomic, transcript (cDNA), and protein sequences in multiple formats
Map genomic coordinates between different assembly versions (e.g., GRCh37 to GRCh38)
Analyze genetic variants using the Variant Effect Predictor (VEP)

Use Cases

Predicting the functional consequences of genetic variants in clinical research
Automating gene annotation pipelines for large-scale genomic datasets
Investigating evolutionary relationships through cross-species ortholog mapping