Ensembl MCP Server

🚀 🧬 Ensembl API MCP Server

A full - featured Model Context Protocol (MCP) server that exposes Ensembl’s REST API.

This server, built using the TypeScript MCP SDK, offers the following advantages:

• Comprehensive coverage: 10 tools map to functional areas instead of 100 + individual endpoints, yet still expose nearly the whole API.
• Production - ready: It uses TypeScript throughout, has 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

🚀 Quick Start

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:

# claude code:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client claude --key your-smithery-secret-key

# cursor:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client cursor --key your-smithery-secret-key

# vscode:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client vscode --key your-smithery-secret-key

# windsurf:
npx -y @smithery/cli@latest install @effieklimi/ensembl-mcp-server --client windsurf --key your-smithery-secret-key

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

# Development with hot reload
npm run dev

# Run tests
npm test

# Production build (optional)
npm run build
npm run start:prod

💻 Usage Examples

Installing via Smithery

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

npx -y @smithery/cli install @effieklimi/ensembl-mcp-server --client claude

📚 Documentation

The ten tools (with endpoints)

1 · ensembl_feature_overlap

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

GET /overlap/region/:species/:region
GET /overlap/id/:id

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

2 · ensembl_regulatory

Regulatory features, binding matrices and related annotations.

GET /overlap/region/:species/:region             (with regulatory filters)
GET /overlap/translation/:id                     (regulatory features on proteins)
GET /species/:species/binding_matrix/:binding_matrix_stable_id

Use cases: TF - binding sites, regulatory annotation.

3 · ensembl_protein_features

Protein - level domains and functional sites.

GET /overlap/translation/:id

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

4 · ensembl_meta

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

GET /info/ping
GET /info/rest
GET /info/software
GET /info/data
GET /info/species
GET /info/divisions
GET /info/assembly/:species
GET /info/biotypes/:species
GET /info/analysis/:species
GET /info/external_dbs/:species
GET /info/variation/:species
GET /archive/id/:id
POST /archive/id

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

5 · ensembl_lookup

Translate IDs ↔ symbols, pull xrefs, recode variants.

GET  /lookup/id/:id
GET  /lookup/symbol/:species/:symbol
POST /lookup/id
POST /lookup/symbol
GET  /xrefs/id/:id
GET  /xrefs/symbol/:species/:symbol
GET  /xrefs/name/:species/:name
GET  /variant_recoder/:species/:id
POST /variant_recoder/:species

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

6 · ensembl_sequence

Retrieve DNA, RNA or protein sequences.

GET  /sequence/id/:id
GET  /sequence/region/:species/:region
POST /sequence/id
POST /sequence/region

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

7 · ensembl_mapping

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

GET /map/cdna/:id/:region
GET /map/cds/:id/:region
GET /map/translation/:id/:region
GET /map/:species/:asm_one/:region/:asm_two

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

8 · ensembl_compara

Comparative genomics—homology, gene trees, alignments.

GET /homology/id/:species/:id
GET /homology/symbol/:species/:symbol
GET /genetree/id/:id
GET /genetree/member/symbol/:species/:symbol
GET /genetree/member/id/:species/:id
GET /cafe/genetree/id/:id
GET /cafe/genetree/member/symbol/:species/:symbol
GET /cafe/genetree/member/id/:species/:id
GET /alignment/region/:species/:region

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

9 · ensembl_variation

Variant lookup, VEP consequences, LD, phenotype mapping.

GET  /variation/:species/:id
GET  /variation/:species/pmcid/:pmcid
GET  /variation/:species/pmid/:pmid
POST /variation/:species
GET  /vep/:species/hgvs/:hgvs_notation
POST /vep/:species/hgvs
GET  /vep/:species/id/:id
POST /vep/:species/id
GET  /vep/:species/region/:region/:allele
POST /vep/:species/region
GET  /ld/:species/:id/:population_name
GET  /phenotype/variant/:species/:id
GET  /phenotype/region/:species/:region
GET  /transcript_haplotypes/:species/:id

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

10 · ensembl_ontotax

Ontology term search and NCBI taxonomy traversal.

GET /ontology/id/:id
GET /ontology/name/:name
GET /taxonomy/id/:id
GET /taxonomy/name/:name

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

🔧 Technical Details

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

🤝 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