🧬 Ensembl API MCP Server

A full-featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API. Built using the TypeScript MCP SDK

• Comprehensive coverage – 10 tools map to functional areas instead of 100 + individual endpoints, yet still expose nearly the whole API.

• Production-ready – TypeScript throughout, robust error handling, and a tidy API-client layer.

• Biologist-friendly – grouped by biological task (genes, variants, compara…), not by low-level REST paths.

Listed on:

• Smithery

• Glama

Use cases:

• 🧬 Gene information – fetch details by ID or symbol

• 🔍 Gene search – scan genes across any species

• 🧬 Sequence retrieval – pull DNA for any genomic region

• 🔬 Variant data – explore variants and their annotations

• 📊 Transcript info – inspect transcripts and isoforms

• 🌍 Multi-species – every species in Ensembl, right here

• 🔗 Cross-references – hop to external databases in one call

• ⚡ Rate-limited – built-in throttling keeps you within Ensembl limits

Installation

Choose your preferred installation method:

Option 1: Via Smithery

1. Visit Smithery - Ensembl MCP Server. The most common platform options include:

Check the MCP's smithery link for additional platform options.

Option 2: Local Development Setup

For development or custom setups:

1. Clone and install dependencies:

   git clone https://github.com/effieklimi/ensembl-mcp-server.git cd ensembl-mcp-server npm install

2. Configure Claude Desktop manually:

   Edit your config file:

   • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json

   • Windows: %APPDATA%/Claude/claude_desktop_config.json

   Add this server configuration:

   { "mcpServers": { "ensembl": { "command": "npm", "args": ["run", "start"], "cwd": "/absolute/path/to/ensembl-mcp-server" } } }

3. Restart Claude Desktop - The Ensembl tools will appear in your available tools

Development Setup

Contributing

We'd love your help! Here's how to get started:

Quick Contact

• Email the dev: effie@effie.bio

Development Workflow

1. Fork the repository

2. Clone your fork:

   git clone https://github.com/YOUR_USERNAME/ensembl-mcp-server.git cd ensembl-mcp-server

3. Install dependencies:

   npm install

4. Run tests to make sure everything works:

   npm test

5. Start development server:

   npm run dev

6. Make your changes and test thoroughly

7. Submit a pull request

Available Scripts

• npm run dev - Development with hot reload

• npm run start - Run the server

• npm test - Run all tests

• npm run build - Compile TypeScript (optional)

• npm run start:prod - Run compiled version

The ten tools (with endpoints)

1 · ensembl_feature_overlap

Find genes, transcripts, or regulatory elements that overlap a region or another feature.

Typical asks: “Which genes sit in chr17:43-44 Mb?” – “What overlaps BRCA1?”

2 · ensembl_regulatory

Regulatory features, binding matrices and related annotations.

Use cases: TF-binding sites, regulatory annotation.

3 · ensembl_protein_features

Protein-level domains and functional sites.

Use cases: protein domains, signal peptides, catalytic residues.

4 · ensembl_meta

Server metadata, species lists, release info, and diagnostics.

Typical asks: “Which assemblies do you have for human?” – server health checks.

5 · ensembl_lookup

Translate IDs ↔ symbols, pull xrefs, recode variants.

Use cases: “What is BRCA1’s Ensembl ID?” – cross-reference UniProt.

6 · ensembl_sequence

Retrieve DNA, RNA or protein sequences.

Use cases: gene FASTA, transcript cDNA, genomic regions.

7 · ensembl_mapping

Coordinate conversion (genome ↔ cDNA/CDS/protein) and assembly lift-over.

Use cases: map CDS to GRCh38, convert protein to genome coords.

8 · ensembl_compara

Comparative genomics—homology, gene trees, alignments.

Use cases: find orthologs, build phylogenies, pull species alignments.

9 · ensembl_variation

Variant lookup, VEP consequences, LD, phenotype mapping.

Use cases: VEP predictions, LD blocks, phenotype associations.

10 · ensembl_ontotax

Ontology term search and NCBI taxonomy traversal.

Use cases: GO term look-up, phenotype ontology, taxonomic classification.

Installing via Smithery

To install ensembl-mcp-server for Claude Desktop automatically via Smithery: