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@cyanheads/ensembl-mcp-server

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

7 Tools • 3 Resources • 1 Prompt

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\n\n[![Version](https://img.shields.io/badge/Version-0.1.3-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-^1.29.0-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-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/)\n\n

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\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

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\n\n**Public Hosted Server:** [https://ensembl.caseyjhand.com/mcp](https://ensembl.caseyjhand.com/mcp)\n\n

\n\n---\n\n## Tools\n\nSeven tools covering the core Ensembl REST API surface — species discovery, gene/transcript lookup, sequence retrieval, genomic region overlap, variant consequence prediction, cross-species homology, and external database cross-references:\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### `ensembl_list_species`\n\nDiscovery tool for the Ensembl species catalog.\n\n- Filter by division: vertebrates, plants, fungi, metazoa, or protists\n- Optional name filter (`nameContains`) for local substring matching\n- Returns display name, common name, assembly, taxon ID, and Ensembl division for each species\n- Required first step — species names like `homo_sapiens` are opaque to non-biologists and are the input format every other tool expects\n\n---\n\n### `ensembl_lookup_gene`\n\nSingle entry point for resolving gene identity.\n\n- Symbol + species lookup (`BRCA2` + `homo_sapiens`) or direct stable ID lookup (`ENSG00000139618`)\n- Batch lookup of up to 20 IDs or symbols in one call via POST endpoints\n- Optional transcript expansion — returns full transcript list with biotype and canonical flag\n- Returns Ensembl stable ID, genomic location (chr:start-end:strand), biotype, description, and transcript list\n- Errors: `not_found` (symbol or ID not in Ensembl), `invalid_species` (call `ensembl_list_species` to discover valid names)\n\n---\n\n### `ensembl_get_sequence`\n\nFetch any sequence type for any Ensembl feature.\n\n- Molecule types: `genomic` (default, includes introns), `cdna` (spliced), `cds` (coding only), `protein`\n- Accepts stable IDs or `species:chr:start-end` region format for genomic region mode\n- Optional flanking sequence (`expand_5prime`, `expand_3prime`) in base pairs\n- Returns sequence with stable ID, molecule type, and character count — large sequences (e.g. BRCA2 at 85,183 bp genomic) returned in full with explicit length so callers can budget context usage\n\n---\n\n### `ensembl_query_region`\n\nFind all genomic features overlapping a chromosomal window.\n\n- Region format: `chr:start-end` (e.g. `13:32315086-32400268`) — no `chr` prefix for vertebrates\n- Feature types: `gene` (default), `transcript`, `variation`, `regulatory`, `exon`\n- Optional biotype filter\n- Defaults to gene only to prevent context overload — a large locus can contain 44,000+ variants when all feature types are selected\n\n---\n\n### `ensembl_predict_variant`\n\nPredict variant consequences via the Ensembl VEP.\n\n- Accepts HGVS notation (transcript-relative: `ENST00000380152.8:c.2T>A`) or genomic region+allele format (`13:32316462:32316462:1/A`)\n- Returns most severe consequence term, affected transcripts and genes, impact level (HIGH/MODERATE/LOW/MODIFIER)\n- Includes colocated known variants with clinical significance (ClinVar, dbSNP)\n- Errors: `invalid_notation` (check format), `not_found` (location outside any known transcript)\n\n---\n\n### `ensembl_get_homology`\n\nCross-species homolog lookup.\n\n- Returns orthologs (default) or paralogs, or both\n- Optional `target_species` filter to narrow to specific organisms\n- Each homolog carries stable ID, species, relationship type (ortholog_one2one, ortholog_one2many, etc.), `perc_id`, `perc_pos`, and taxonomy level\n\n---\n\n### `ensembl_get_xrefs`\n\nFull cross-database reference set for any Ensembl feature.\n\n- Returns all external IDs by default: HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and more (56 xrefs for BRCA2)\n- Optional `dbname` filter (e.g. `HGNC`, `Uniprot_gn`, `EntrezGene`, `MIM_GENE`) to narrow output\n- Uses the `xrefs/id` endpoint (not `xrefs/symbol`) — returns the full cross-reference set\n- IDs returned here chain directly to protein, literature, disease, and pathway resources in other MCP servers\n\n## Resources and prompts\n\n| Type | Name | Description |\n|:-----|:-----|:------------|\n| Resource | `ensembl://gene/{id}` | Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list |\n| Resource | `ensembl://transcript/{id}` | Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length |\n| Resource | `ensembl://species` | Full list of supported Ensembl species with name, display name, assembly, taxon ID, and division |\n| Prompt | `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs |\n\nAll resource data is also reachable via tools. The `ensembl://species` resource provides the full species catalog with cursor pagination; `ensembl_list_species` is the tool equivalent with filtering support.\n\n## Features\n\nBuilt on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):\n\n- Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation\n- Unified error handling — handlers throw, framework catches, classifies, and formats\n- Pluggable auth: `none`, `jwt`, `oauth`\n- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`\n- Structured logging with optional OpenTelemetry tracing\n- STDIO and Streamable HTTP transports\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: tracks `x-ratelimit-remaining`, retries 429 with `Retry-After`, and retries transient 5xx\n- Batch POST endpoints used throughout — `POST /lookup/id` (up to 50 IDs) and `POST /lookup/symbol/{species}` 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- Sequence character count stated on every `ensembl_get_sequence` response so callers can budget context before consuming large genomic sequences\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 the full 7-tool 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 v1.3.11](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_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`](https://github.com/cyanheads/ensembl-mcp-server/blob/main/.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`](https://github.com/cyanheads/ensembl-mcp-server/blob/main/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 and pull requests 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](https://github.com/cyanheads/ensembl-mcp-server/blob/main/LICENSE) for details.\n","changelogMarkdown","videoKey","requiredSecretsJson","publishedAt","priceCents","trialDays",0,"categoryDisplayName","Developer Tools","upstream",{"_95":96,"_97":98,"_99":100,"_101":102,"_103":104},"requiredSecrets",[],"tags",[],"assets",[],"stats",{"_93":80,"_94":80},"ratingAvg","reviewCount","topics",[105,106,107,19,108,109,110,111,112,113,114],"license","Apache-2.0","language","TypeScript","registryName","io.github.cyanheads/ensembl-mcp-server","homepage","https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server","ai-agents","ai-tools","bioinformatics","ensembl","genes","genomics","mcp","mcp-server","model-context-protocol","typescript","ENV",{"_117":118,"_119":120,"_121":122},"ENVIRONMENT","production","TURNSTILE_SITE_KEY","0x4AAAAAAB8-rEI2gNDf_QhU","SENTRY_DSN","https://45fd1229f78089d5c3ee78be128030e1@o4510583261757440.ingest.de.sentry.io/4510584253448272"]