Agent skill · research science · aiskillstore
ensembl-database
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
Why this skill is useful
Provides specific commands and patterns for querying the Ensembl REST API that the AI wouldn't reliably generate on its own.
What it needs
Requires ensembl_rest installed locally. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
Ensembl Database Overview Access and query the Ensembl genome database, a comprehensive resource for vertebrate genomic data maintained by EMBL-EBI. The database provides gene annotations, sequences, variants, regulatory information, and comparative genomics data for over 250 species. Current release is 115 (September 2025). When to Use This Skill This skill should be used when: Querying gene information by symbol or Ensembl ID Retrieving DNA, transcript, or protein sequences Analyzing genetic variants using the Variant Effect Predictor (VEP) Finding orthologs and paralogs across species Accessing regulatory features and genomic annotations Converting coordinates between genome assemblies (e.g., GRCh37 to GRCh38) Performing comparative genomics analyses Integrating Ensembl data into genomic research pipelines Core Capabilities 1. Gene Information Retrieval Query gene data by symbol, Ensembl ID, or external database identifiers. Common operations: Look up gene information by symbol (e.g., "BRCA2", "TP53") Retrieve transcript and protein information Get gene coordinates and chromosomal locations Access cross-references to external databases (UniProt, RefSeq, etc.) Using the ensemblrest package: Direct REST API (no package): 2. Sequence Retrieval Fetch genomic, transcript, or protein sequences in various formats (JSON, FASTA, plain text). Operations: Get DNA sequences for genes or genomic regions Retrieve transcript sequences (cDNA) Access protein sequences Extract sequences with flanking regions or modifications Example: 3. Variant Analysis Query genetic variation data and predict variant consequences using the Variant Effect Predictor (VEP). Capabilities: Look up variants by rsID or genomic coordinates Predict functional consequences of variants Access population frequency data Retrieve phenotype associations VEP example: 4. Comparative Genomics Perform cross-species comparisons to identify orthologs, paralogs, and evolutionary relationships. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/ensembl-database