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\n

@cyanheads/ensembl-mcp-server

\n

Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.\n

7 Tools • 4 Resources • 1 Prompt
\n

\n
\n\n
\n\n[![Version](https://img.shields.io/badge/Version-0.5.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)\n\n
\n\n
\n\n[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/ensembl-mcp-server/releases/latest/download/ensembl-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=ensembl-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvZW5zZW1ibC1tY3Atc2VydmVyIl19) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](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)\n\n[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)\n\n
\n\n
\n\n**Public Hosted Server:** [https://ensembl.caseyjhand.com/mcp](https://ensembl.caseyjhand.com/mcp)\n\n
\n\n---\n\n## Overview\n\nGene, sequence, and variant data for vertebrates and other model organisms from the Ensembl REST API. Look up genes, fetch sequences, predict variant consequences, find orthologs, and cross-reference external databases from any MCP client. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.\n\n### Tools\n\n| Tool | Description |\n|:-----|:------------|\n| `ensembl_list_species` | List species supported by Ensembl with display name, common name, assembly, taxon ID, and division |\n| `ensembl_lookup_gene` | Resolve a gene by symbol + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list |\n| `ensembl_get_sequence` | Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region |\n| `ensembl_query_region` | Find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region |\n| `ensembl_predict_variant` | Predict functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP) |\n| `ensembl_get_homology` | Find orthologs and/or paralogs of a gene across species with percent identity and taxonomy level |\n| `ensembl_get_xrefs` | Retrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others |\n\n### Resources\n\n| Resource | Description |\n|:---|:---|\n| `ensembl://gene/{id}` | Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list |\n| `ensembl://transcript/{id}` | Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length |\n| `ensembl://species` | Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint) |\n| `ensembl://species/{division}` | Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) |\n\nAll resource data is also reachable via the `ensembl_list_species` tool, which additionally filters by name.\n\n### Prompts\n\n| Prompt | Description |\n|:---|:---|\n| `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs |\n\n## Capability reference\n\n### `ensembl_list_species` tool\n\n- Filter by division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) or `nameContains` for a local substring match against name, display name, and common name\n- Omit `division` to return the endpoint default division (vertebrates, ~356 species on the default GRCh38 endpoint)\n- Returns internal name (the value every other tool expects), display name, common name, taxon ID, assembly, and division\n- Required first step — species names like `homo_sapiens` are opaque to non-biologists\n\n---\n\n### `ensembl_lookup_gene` tool\n\n- Exactly one of `symbol` (+ optional `species`, default `homo_sapiens`), `id`, `ids` (batch, up to 20), or `symbols` (batch, up to 20)\n- `expand_transcripts` (default `false`) adds the full transcript list with biotype and canonical flag\n- Batch modes (`ids`/`symbols`) return a `succeeded`/`failed` split with per-item error strings instead of failing the call\n- Errors: `not_found`, `invalid_species`, `no_input`, `conflicting_input`\n\n---\n\n### `ensembl_get_sequence` tool\n\n- `type`: `genomic` (default, includes introns), `cdna` (spliced), `cds` (coding only), `protein`\n- Accepts a stable ID (`ENSG…`/`ENST…`/`ENSP…`) or a region — `species:chr:start-end`, or bare `chr:start-end` with `species` set; a region spans at most 10,000,000 bases, with start at or below end\n- `expand_5prime` / `expand_3prime` (default `0`) extend flanking base pairs for genomic and region queries\n- `protein` and `cds` require a transcript or protein ID, not a gene ID; region ids are genomic-only\n- Returns a bounded window: `offset` (0-based, default `0`) and `max_length` (default `10000`, `0` for the rest uncapped) index the resolved sequence, flanks included\n- `length` is always the full sequence length; `truncated` and `nextOffset` say whether more follows and where to resume, so walking `nextOffset` reconstructs the whole sequence\n- Errors: `not_found`, `type_mismatch`, `missing_species`, `invalid_region`\n\n---\n\n### `ensembl_query_region` tool\n\n- `region` in `chr:start-end` format, at most 5,000,000 bases; `feature` array (at least one) defaults to `[\"gene\"]`, also accepts `transcript`, `variation`, `regulatory`, `exon`; optional `biotype` filter\n- Defaults to genes only — requesting `variation` on a large locus can match 44,000+ features\n- `max_results` caps the feature list (default `100`, `0` uncapped); `totalCount` always reports the true count found\n- `assemblyName` (e.g. `GRCh38`) names the assembly the coordinates are on\n- Exon rows carry a `parentId` and `rank`, since one exon is reported once per parent transcript\n- Errors: `invalid_region`, `invalid_species`\n\n---\n\n### `ensembl_predict_variant` tool\n\n- `variant` accepts HGVS (transcript-relative or genomic), region+allele (`chr:start:end:strand/allele`), or a dbSNP rsID\n- `max_transcript_consequences` (default `10`) and `max_pubmed_ids_per_variant` (default `10`) cap large VEP results; set either to `0` for the full set, or `include_all_colocated_pubmed: true` for uncapped PubMed IDs\n- Returns most severe consequence term, per-transcript impact (HIGH/MODERATE/LOW/MODIFIER), and colocated known variants with clinical significance\n- Totals (`transcriptConsequencesTotal`, `pubmedTotal`) are always reported even when capped\n- Errors: `invalid_notation`, `not_found`\n\n---\n\n### `ensembl_get_homology` tool\n\n- Exactly one of `symbol` (+ `species`, default `homo_sapiens`) or `id`; optional `target_species` filter\n- `type`: `orthologues` (default), `paralogues`, or `all`\n- `max_results` caps the homolog list (default `25`, `0` uncapped); `totalCount` always reports the true count available\n- Errors: `not_found`, `no_input`, `conflicting_input`\n\n---\n\n### `ensembl_get_xrefs` tool\n\n- `id` (`ENSG…`/`ENST…`) required; optional `dbname` filter (e.g. `HGNC`, `Uniprot_gn`, `EntrezGene`, `MIM_GENE`, `RefSeq_mRNA`, `Reactome`, `GO`)\n- Uses the `xrefs/id` endpoint, returning the full cross-reference set (56+ entries for well-annotated genes like BRCA2)\n- Errors: `not_found`\n\n---\n\n### `ensembl://gene/{id}` resource\n\n- Returns location, biotype, description, and transcript list for a gene stable ID (`ENSG…`); version suffix optional\n- Errors: `not_found`\n\n---\n\n### `ensembl://transcript/{id}` resource\n\n- Returns parent gene, location, biotype, canonical flag, and length for a transcript stable ID (`ENST…`); version suffix optional\n- Errors: `not_found`\n\n---\n\n### `ensembl://species` resource\n\n- No parameters — returns the endpoint default division (vertebrates, ~356 species on the default GRCh38 endpoint)\n- For a named division, read `ensembl://species/{division}` instead\n\n---\n\n### `ensembl://species/{division}` resource\n\n- `division` required: `EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, or `EnsemblProtists`\n\n---\n\n### `ensembl_gene_dossier` prompt\n\n- Arguments: `gene_symbol` required; `species` optional (default `homo_sapiens`)\n- Sequences a 7-step workflow: resolve the gene → fetch the protein sequence → find variants in the locus → predict variant consequences → find cross-species orthologs → get external database IDs → synthesize the dossier\n\n## Features\n\nBuilt on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core): stdio and Streamable HTTP transports, pluggable auth (`none` / `jwt` / `oauth`), swappable storage (`in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`), structured logging with optional OpenTelemetry tracing.\n\nEnsembl-specific:\n\n- Keyless REST API — no API key required; Ensembl REST is fully public at 55,000 req/hr\n- Rate-limit-aware service layer: retries 429 honoring `Retry-After`, and retries transient 5xx and HTML error pages\n- Batch POST endpoints used throughout — `POST /lookup/id` and `POST /lookup/symbol/{species}` (up to 1,000 items each upstream) reduce N+1 round trips in multi-gene workflows\n- GRCh37 legacy support via `ENSEMBL_BASE_URL` — point the entire server at `https://grch37.rest.ensembl.org` for clinical workflows on the older assembly\n- All coordinate-bearing responses echo the assembly name so agents never see a bare genomic position without assembly context\n\nAgent-friendly output:\n\n- `ensembl_get_sequence` returns sequences in bounded windows (10,000 characters by default) with the full length and a `nextOffset` to continue, so a long gene or locus never lands in one response unasked\n- `ensembl_list_species` is explicitly the discovery step — tool descriptions call out the opaque internal-name format and direct agents to it before using species-dependent tools\n- 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 all 6 tools into one research workflow\n\n## Getting started\n\n### Public Hosted Instance\n\nA public instance is available at `https://ensembl.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:\n\n```json\n{\n \"mcpServers\": {\n \"ensembl-mcp-server\": {\n \"type\": \"streamable-http\",\n \"url\": \"https://ensembl.caseyjhand.com/mcp\"\n }\n }\n}\n```\n\n### Self-Hosted / Local\n\nAdd the following to your MCP client configuration file.\n\n```json\n{\n \"mcpServers\": {\n \"ensembl-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"bunx\",\n \"args\": [\"@cyanheads/ensembl-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with npx (no Bun required):\n\n```json\n{\n \"mcpServers\": {\n \"ensembl-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"npx\",\n \"args\": [\"-y\", \"@cyanheads/ensembl-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with Docker:\n\n```json\n{\n \"mcpServers\": {\n \"ensembl-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"docker\",\n \"args\": [\n \"run\", \"-i\", \"--rm\",\n \"-e\", \"MCP_TRANSPORT_TYPE=stdio\",\n \"ghcr.io/cyanheads/ensembl-mcp-server:latest\"\n ]\n }\n }\n}\n```\n\nFor Streamable HTTP, set the transport and start the server:\n\n```sh\nMCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http\n# Server listens at http://localhost:3010/mcp\n```\n\n### Prerequisites\n\n- [Bun v1.4.0](https://bun.sh/) or higher (or Node.js v24+).\n- No API key required — Ensembl REST is fully public.\n\n### Installation\n\n1. **Clone the repository:**\n\n```sh\ngit clone https://github.com/cyanheads/ensembl-mcp-server.git\n```\n\n2. **Navigate into the directory:**\n\n```sh\ncd ensembl-mcp-server\n```\n\n3. **Install dependencies:**\n\n```sh\nbun install\n```\n\n4. **Configure environment:**\n\n```sh\ncp .env.example .env\n# edit .env if you need to override ENSEMBL_BASE_URL (e.g. for GRCh37)\n```\n\n## Configuration\n\nAll configuration is validated at startup via Zod schemas in `src/config/server-config.ts`.\n\n| Variable | Description | Default |\n|:---------|:------------|:--------|\n| `ENSEMBL_BASE_URL` | Ensembl REST API base URL. Override for GRCh37 (`https://grch37.rest.ensembl.org`) or a local mirror. | `https://rest.ensembl.org` |\n| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http` | `stdio` |\n| `MCP_HTTP_PORT` | HTTP server port | `3010` |\n| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path | `/mcp` |\n| `MCP_SESSION_MODE` | HTTP session mode: `auto`, `stateful`, or `stateless`. Schema default `auto` resolves to stateful; this server explicitly uses stateless. | `stateless` |\n| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |\n| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |\n| `LOGS_DIR` | Directory for log files (Node.js only) | `/logs` |\n| `OTEL_ENABLED` | Enable OpenTelemetry | `false` |\n\nSee [`.env.example`](./.env.example) for the full list of optional overrides.\n\n## Running the server\n\n### Local development\n\n- **Build and run:**\n\n ```sh\n # One-time build\n bun run rebuild\n\n # Run the built server\n bun run start:stdio\n # or\n bun run start:http\n ```\n\n- **Run checks and tests:**\n\n ```sh\n bun run devcheck # Lint, format, typecheck, security\n bun run test # Vitest test suite\n bun run lint:mcp # Validate MCP definitions against spec\n ```\n\n### Docker\n\n```sh\ndocker build -t ensembl-mcp-server .\ndocker run --rm -p 3010:3010 ensembl-mcp-server\n```\n\nThe Dockerfile defaults to HTTP transport, stateless session mode, and logs to `/var/log/ensembl-mcp-server`. OpenTelemetry peer dependencies are installed by default — build with `--build-arg OTEL_ENABLED=false` to omit them.\n\n## Project structure\n\n| Directory | Purpose |\n|:----------|:--------|\n| `src/index.ts` | `createApp()` entry point — registers tools/resources/prompts and inits services |\n| `src/config` | Server-specific environment variable parsing and validation with Zod |\n| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`) — 7 tools |\n| `src/mcp-server/resources` | Resource definitions (`*.resource.ts`) — gene, transcript, species |\n| `src/mcp-server/prompts` | Prompt definitions (`*.prompt.ts`) — gene dossier workflow |\n| `src/services/ensembl` | Ensembl REST API client — HTTP, rate-limit handling, retry, error normalization |\n| `tests/` | Unit and integration tests mirroring `src/` |\n\n## Development guide\n\nSee [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:\n\n- Handlers throw, framework catches — no `try/catch` in tool logic\n- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage\n- Register new tools and resources in the `createApp()` arrays in `src/index.ts`\n- Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields\n\n## Contributing\n\nIssues are welcome. Run checks and tests before submitting:\n\n```sh\nbun run devcheck\nbun run test\n```\n\n## License\n\nApache-2.0 — see [LICENSE](LICENSE) for details.\n","readmeFilename":"README.md"}