# ensembl-mcp-server [Health: Active]
**Category:** π» Developer Tools
**Repository:** https://github.com/cyanheads/ensembl-mcp-server
**GitHub Stars:** 2
**Views:** 0
**Installs:** 0
**Upvotes:** 0
**Directory Page:** https://allmcps.com/mcp/ensembl-mcp-server
## Description
Look up genes, fetch sequences, predict variant consequences, find orthologs and xrefs via Ensembl.
## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `bunx` (confidence: high):
```json
"mcpServers": {
"ensembl-mcp-server": {
"command": "bunx",
"args": ["@cyanheads/ensembl-mcp-server@latest"]
}
}
```
## Documentation & README
@cyanheads/ensembl-mcp-server
Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.
7 Tools β’ 4 Resources β’ 1 Prompt
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
[](https://github.com/cyanheads/ensembl-mcp-server/releases/latest/download/ensembl-mcp-server.mcpb) [](https://cursor.com/en/install-mcp?name=ensembl-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvZW5zZW1ibC1tY3Atc2VydmVyIl19) [](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22ensembl-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fensembl-mcp-server%22%5D%7D)
[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
**Public Hosted Server:** [https://ensembl.caseyjhand.com/mcp](https://ensembl.caseyjhand.com/mcp)
---
## Tools
Seven tools covering the core Ensembl REST API surface β species discovery, gene/transcript lookup, sequence retrieval, genomic region overlap, variant consequence prediction, cross-species homology, and external database cross-references:
| Tool | Description |
|:-----|:------------|
| `ensembl_list_species` | List species supported by Ensembl with display name, common name, assembly, taxon ID, and division |
| `ensembl_lookup_gene` | Resolve a gene by symbol + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list |
| `ensembl_get_sequence` | Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region |
| `ensembl_query_region` | Find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region |
| `ensembl_predict_variant` | Predict functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP) |
| `ensembl_get_homology` | Find orthologs and/or paralogs of a gene across species with percent identity and taxonomy level |
| `ensembl_get_xrefs` | Retrieve cross-database references for a gene β HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others |
### `ensembl_list_species`
Discovery tool for the Ensembl species catalog.
- Filter by division: vertebrates, plants, fungi, metazoa, or protists
- Optional name filter (`nameContains`) for local substring matching
- Returns display name, common name, assembly, taxon ID, and Ensembl division for each species
- Required first step β species names like `homo_sapiens` are opaque to non-biologists and are the input format every other tool expects
---
### `ensembl_lookup_gene`
Single entry point for resolving gene identity.
- Symbol + species lookup (`BRCA2` + `homo_sapiens`) or direct stable ID lookup (`ENSG00000139618`)
- Batch lookup of up to 20 IDs or symbols in one call via POST endpoints
- Optional transcript expansion β returns full transcript list with biotype and canonical flag
- Returns Ensembl stable ID, genomic location (chr:start-end:strand), biotype, description, and transcript list
- Errors: `not_found` (symbol or ID not in Ensembl), `invalid_species` (call `ensembl_list_species` to discover valid names)
---
### `ensembl_get_sequence`
Fetch any sequence type for any Ensembl feature.
- Molecule types: `genomic` (default, includes introns), `cdna` (spliced), `cds` (coding only), `protein`
- Accepts stable IDs or `species:chr:start-end` region format for genomic region mode
- Optional flanking sequence (`expand_5prime`, `expand_3prime`) in base pairs
- Returns sequence with stable ID, molecule type, and character count β large sequences (e.g. BRCA2 at 85,183 bp genomic) returned in full with explicit length so callers can budget context usage
---
### `ensembl_query_region`
Find all genomic features overlapping a chromosomal window.
- Region format: `chr:start-end` (e.g. `13:32315086-32400268`) β no `chr` prefix for vertebrates
- Feature types: `gene` (default), `transcript`, `variation`, `regulatory`, `exon`
- Optional biotype filter
- Defaults to gene only to prevent context overload β a large locus can contain 44,000+ variants when all feature types are selected
---
### `ensembl_predict_variant`
Predict variant consequences via the Ensembl VEP.
- Accepts HGVS notation (transcript-relative: `ENST00000380152.8:c.2T>A`) or genomic region+allele format (`13:32316462:32316462:1/A`)
- Returns most severe consequence term, affected transcripts and genes, impact level (HIGH/MODERATE/LOW/MODIFIER)
- Includes colocated known variants with clinical significance (ClinVar, dbSNP)
- Errors: `invalid_notation` (check format), `not_found` (location outside any known transcript)
---
### `ensembl_get_homology`
Cross-species homolog lookup.
- Returns orthologs (default) or paralogs, or both
- Optional `target_species` filter to narrow to specific organisms
- Each homolog carries stable ID, species, relationship type (ortholog_one2one, ortholog_one2many, etc.), `perc_id`, `perc_pos`, and taxonomy level
---
### `ensembl_get_xrefs`
Full cross-database reference set for any Ensembl feature.
- Returns all external IDs by default: HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and more (56 xrefs for BRCA2)
- Optional `dbname` filter (e.g. `HGNC`, `Uniprot_gn`, `EntrezGene`, `MIM_GENE`) to narrow output
- Uses the `xrefs/id` endpoint (not `xrefs/symbol`) β returns the full cross-reference set
- IDs returned here chain directly to protein, literature, disease, and pathway resources in other MCP servers
## Resources and prompts
| Type | Name | Description |
|:-----|:-----|:------------|
| Resource | `ensembl://gene/{id}` | Gene record by stable ID (`ENSGβ¦`) β location, biotype, description, and transcript list |
| Resource | `ensembl://transcript/{id}` | Transcript record by stable ID (`ENSTβ¦`) β parent gene, location, biotype, canonical flag, and length |
| Resource | `ensembl://species` | Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint) with name, display name, assembly, taxon ID, and division |
| Resource | `ensembl://species/{division}` | Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) |
| Prompt | `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol β ID + location β sequence β variants β orthologs β xrefs |
All resource data is also reachable via tools. `ensembl://species` returns the endpoint default division (vertebrates) and `ensembl://species/{division}` returns a named division; `ensembl_list_species` is the tool equivalent, filtering by division and name.
## Features
Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):
- Declarative tool, resource, and prompt definitions β single file per primitive, framework handles registration and validation
- Unified error handling β handlers throw, framework catches, classifies, and formats
- Pluggable auth: `none`, `jwt`, `oauth`
- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
- Structured logging with optional OpenTelemetry tracing
- STDIO and Streamable HTTP transports
Ensembl-specific:
- Keyless REST API β no API key required; Ensembl REST is fully public at 55,000 req/hr
- Rate-limit-aware service layer: tracks `x-ratelimit-remaining`, retries 429 with `Retry-After`, and retries transient 5xx
- Batch POST endpoints used throughout β `POST /lookup/id` (up to 50 IDs) and `POST /lookup/symbol/{species}` reduce N+1 round trips in multi-gene workflows
- GRCh37 legacy support via `ENSEMBL_BASE_URL` β point the entire server at `https://grch37.rest.ensembl.org` for clinical workflows on the older assembly
- All coordinate-bearing responses echo the assembly name so agents never see a bare genomic position without assembly context
Agent-friendly output:
- Sequence character count stated on every `ensembl_get_sequence` response so callers can budget context before consuming large genomic sequences
- `ensembl_list_species` is explicitly the discovery step β tool descriptions call out the opaque internal-name format and direct agents to it before using species-dependent tools
- Cross-tool chaining made explicit: xref IDs from `ensembl_get_xrefs` are described as inputs for protein and literature servers; the `ensembl_gene_dossier` prompt sequences the full 7-tool research workflow
## Getting started
### Public Hosted Instance
A public instance is available at `https://ensembl.caseyjhand.com/mcp` β no installation required. Point any MCP client at it via Streamable HTTP:
```json
{
"mcpServers": {
"ensembl-mcp-server": {
"type": "streamable-http",
"url": "https://ensembl.caseyjhand.com/mcp"
}
}
}
```
### Self-Hosted / Local
Add the following to your MCP client configuration file.
```json
{
"mcpServers": {
"ensembl-mcp-server": {
"type": "stdio",
"command": "bunx",
"args": ["@cyanheads/ensembl-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info"
}
}
}
}
```
Or with npx (no Bun required):
```json
{
"mcpServers": {
"ensembl-mcp-server": {
"type": "stdio",
"command": "npx",
"args": ["-y", "@cyanheads/ensembl-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info"
}
}
}
}
```
Or with Docker:
```json
{
"mcpServers": {
"ensembl-mcp-server": {
"type": "stdio",
"command": "docker",
"args": [
"run", "-i", "--rm",
"-e", "MCP_TRANSPORT_TYPE=stdio",
"ghcr.io/cyanheads/ensembl-mcp-server:latest"
]
}
}
}
```
For Streamable HTTP, set the transport and start the server:
```sh
MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp
```
### Prerequisites
- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).
- No API key required β Ensembl REST is fully public.
### Installation
1. **Clone the repository:**
```sh
git clone https://github.com/cyanheads/ensembl-mcp-server.git
```
2. **Navigate into the directory:**
```sh
cd ensembl-mcp-server
```
3. **Install dependencies:**
```sh
bun install
```
4. **Configure environment:**
```sh
cp .env.example .env
# edit .env if you need to override ENSEMBL_BASE_URL (e.g. for GRCh37)
```
## Configuration
All configuration is validated at startup via Zod schemas in `src/config/server-config.ts`.
| Variable | Description | Default |
|:---------|:------------|:--------|
| `ENSEMBL_BASE_URL` | Ensembl REST API base URL. Override for GRCh37 (`https://grch37.rest.ensembl.org`) or a local mirror. | `https://rest.ensembl.org` |
| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http` | `stdio` |
| `MCP_HTTP_PORT` | HTTP server port | `3010` |
| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path | `/mcp` |
| `MCP_SESSION_MODE` | HTTP session mode: `auto`, `stateful`, or `stateless`. Schema default `auto` resolves to stateful; this server explicitly uses stateless. | `stateless` |
| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |
| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |
| `LOGS_DIR` | Directory for log files (Node.js only) | `/logs` |
| `OTEL_ENABLED` | Enable OpenTelemetry | `false` |
See [`.env.example`](https://github.com/cyanheads/ensembl-mcp-server/blob/HEAD/.env.example) for the full list of optional overrides.
## Running the server
### Local development
- **Build and run:**
```sh
# One-time build
bun run rebuild
# Run the built server
bun run start:stdio
# or
bun run start:http
```
- **Run checks and tests:**
```sh
bun run devcheck # Lint, format, typecheck, security
bun run test # Vitest test suite
bun run lint:mcp # Validate MCP definitions against spec
```
### Docker
```sh
docker build -t ensembl-mcp-server .
docker run --rm -p 3010:3010 ensembl-mcp-server
```
The Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/ensembl-mcp-server`. OpenTelemetry peer dependencies are installed by default β build with `--build-arg OTEL_ENABLED=false` to omit them.
## Project structure
| Directory | Purpose |
|:----------|:--------|
| `src/index.ts` | `createApp()` entry point β registers tools/resources/prompts and inits services |
| `src/config` | Server-specific environment variable parsing and validation with Zod |
| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`) β 7 tools |
| `src/mcp-server/resources` | Resource definitions (`*.resource.ts`) β gene, transcript, species |
| `src/mcp-server/prompts` | Prompt definitions (`*.prompt.ts`) β gene dossier workflow |
| `src/services/ensembl` | Ensembl REST API client β HTTP, rate-limit handling, retry, error normalization |
| `tests/` | Unit and integration tests mirroring `src/` |
## Development guide
See [`CLAUDE.md`](https://github.com/cyanheads/ensembl-mcp-server/blob/HEAD/CLAUDE.md) for development guidelines and architectural rules. The short version:
- Handlers throw, framework catches β no `try/catch` in tool logic
- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage
- Register new tools and resources in the `createApp()` arrays in `src/index.ts`
- Wrap external API calls: validate raw β normalize to domain type β return output schema; never fabricate missing fields
## Contributing
Issues and pull requests are welcome. Run checks and tests before submitting:
```sh
bun run devcheck
bun run test
```
## License
Apache-2.0 β see [LICENSE](https://github.com/cyanheads/ensembl-mcp-server/blob/HEAD/LICENSE) for details.