What species are supported by the Ensembl Database skill?

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

How does the skill handle Ensembl API rate limits?

The skill is designed to respect the Ensembl REST API limit of 15 requests per second and includes logic to handle 429 'Too Many Requests' responses by checking the Retry-After header.

Can I use this skill to convert genomic coordinates?

Yes, the skill provides assembly mapping capabilities to convert coordinates between different genome versions, such as mapping from GRCh37 (hg19) to GRCh38.

Does this skill support the Variant Effect Predictor (VEP)?

Yes, the skill includes core capabilities for querying VEP to predict the functional consequences of genetic variants using HGVS notation or rsIDs.

Do I need any specific Python packages to use this skill?

While it can work with standard libraries like 'requests', it is recommended to have 'ensembl_rest' installed for a more robust and Pythonic interface to the API endpoints.

Ensembl Genome Database Integration

Name: Ensembl Genome Database Integration
Author: Activer007

byActiver007

0•

データサイエンスとML

Queries the Ensembl REST API to retrieve genomic annotations, sequences, and variant data for over 250 vertebrate species.

The Ensembl Database skill provides a specialized interface for programmatically interacting with the EMBL-EBI Ensembl genome database, a premier resource for vertebrate genomic data. It enables researchers and developers to perform complex biological queries including gene symbol lookups, multi-format sequence retrieval, and functional variant analysis via the Variant Effect Predictor (VEP). By streamlining access to comparative genomics, ortholog mapping, and assembly coordinate conversions (such as GRCh37 to GRCh38), this skill significantly accelerates the development of bioinformatics pipelines and genomic research workflows within the Claude environment.

主な機能

01Multi-format sequence retrieval for DNA, cDNA, and proteins

02Comparative genomics for identifying orthologs and paralogs

03Gene and transcript annotation lookup by symbol or Ensembl ID

04Genomic coordinate conversion between GRCh37 and GRCh38 assemblies

05Variant Effect Predictor (VEP) for functional consequence mapping

060 GitHub stars

ユースケース

01Analyzing genetic variants and predicting their functional impact on protein coding

02Building automated bioinformatics pipelines for gene annotation and data extraction

03Mapping evolutionary relationships and conservation across multiple vertebrate species

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills ensembl-database

For use in Claude.ai and ChatGPT

主な機能

01Multi-format sequence retrieval for DNA, cDNA, and proteins

02Comparative genomics for identifying orthologs and paralogs

03Gene and transcript annotation lookup by symbol or Ensembl ID

04Genomic coordinate conversion between GRCh37 and GRCh38 assemblies

05Variant Effect Predictor (VEP) for functional consequence mapping

060 GitHub stars

ユースケース

01Analyzing genetic variants and predicting their functional impact on protein coding

02Building automated bioinformatics pipelines for gene annotation and data extraction

03Mapping evolutionary relationships and conservation across multiple vertebrate species