ensembl-database
Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
npx skills add BioTender-max/awesome-bio-agent-skills --skill ensembl-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Ensembl Genome Database ## Overview Ensembl is a comprehensive genome annotation database covering 300+ vertebrate and non-vertebrate species. The Ensembl REST API provides programmatic access to gene models, transcript/protein sequences, variant annotations, cross-references, regulatory features, and comparative genomics without requiring any login or API key. ## When to Use - Retrieving official gene and transcript annotations (stable IDs, biotype, genomic coordinates) for human or model organism genes - Converting between gene identifier namespaces (HGNC symbol ↔ Ensembl ID ↔ RefSeq ↔ UniProt) - Fetching genomic or cDNA/CDS/protein sequences for a gene or transcript - Looking up variant consequences and functional impact (VEP) for a list of SNPs - Querying regulatory features (promoters, enhancers, CTCF sites) in a genomic region - Performing comparative genomics queries (orthologs, paralogs, gene trees) across species - For local offline access to large genomic annotations, use `pyensembl` instead - For pathway and metabolic annotations, use `kegg-database` or `reactome-database` instead ## Prerequisites - **Python packages**: `requests` - **Data requirements**: gene symbols,
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: Gene Lookup by Symbol or Stable ID
- Query 2: Batch Lookup
- Query 3: Sequence Retrieval
- Query 4: Cross-References (ID Mapping)
- Query 5: Variant Consequence Annotation (VEP)
- Query 6: Regulatory Features
- Query 7: Comparative Genomics (Orthologs / Gene Trees)
- Key Concepts
- Stable IDs and Versioning
pip install requests
What does the ensembl-database skill do?
Ensembl REST API for gene/transcript/variant annotations in 300+ species. Gene info by symbol/ID, sequence, cross-refs (HGNC, RefSeq, UniProt), regulatory features. For bulk local use pyensembl; for pathways use kegg-database.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill ensembl-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.