@cyanheads/ensembl-mcp-server 0.1.1

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package/README.md

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+<div align="center">
+  <h1>@cyanheads/ensembl-mcp-server</h1>
+  <p><b>Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.</b>
+  <div>7 Tools • 3 Resources • 1 Prompt</div>
+  </p>
+</div>
+
+<div align="center">
+
+[![Version](https://img.shields.io/badge/Version-0.1.1-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/)
+
+</div>
+
+<div align="center">
+
+[![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)
+
+[![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)
+
+</div>
+
+---
+
+## Tools
+
+Seven 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:
+
+| 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 — 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 — 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 — 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 — 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`) — no `chr` prefix for vertebrates
+- Feature types: `gene` (default), `transcript`, `variation`, `regulatory`, `exon`
+- Optional biotype filter
+- Defaults to gene only to prevent context overload — 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`) — 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 (`ENSG…`) — location, biotype, description, and transcript list |
+| Resource | `ensembl://transcript/{id}` | Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length |
+| Resource | `ensembl://species` | Full list of supported Ensembl species with name, display name, assembly, taxon ID, and division |
+| Prompt | `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs |
+
+All 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.
+
+## Features
+
+Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):
+
+- Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
+- Unified error handling — 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 — 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 — `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` — 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 — 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
+
+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 v1.3.11](https://bun.sh/) or higher (or Node.js v24+).
+- No API key required — 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_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) | `<project-root>/logs` |
+| `OTEL_ENABLED` | Enable OpenTelemetry | `false` |
+
+See [`.env.example`](./.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 — build with `--build-arg OTEL_ENABLED=false` to omit them.
+
+## Project structure
+
+| Directory | Purpose |
+|:----------|:--------|
+| `src/index.ts` | `createApp()` entry point — 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`) — 7 tools |
+| `src/mcp-server/resources` | Resource definitions (`*.resource.ts`) — gene, transcript, species |
+| `src/mcp-server/prompts` | Prompt definitions (`*.prompt.ts`) — gene dossier workflow |
+| `src/services/ensembl` | Ensembl REST API client — HTTP, rate-limit handling, retry, error normalization |
+| `tests/` | Unit and integration tests mirroring `src/` |
+
+## Development guide
+
+See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
+
+- Handlers throw, framework catches — 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 → normalize to domain type → 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 — see [LICENSE](LICENSE) for details.

package/changelog/0.1.x/0.1.1.md

@@ -0,0 +1,31 @@
+---
+summary: "Initial public release — 7 tools, 3 resources, 1 prompt over the Ensembl REST API; security hardening strips internal URL from error data"
+breaking: false
+security: true
+---
+
+# 0.1.1 — 2026-06-05
+
+Initial public release of `@cyanheads/ensembl-mcp-server`. Provides 7 tools, 3 resources, and 1 prompt over the [Ensembl REST API](https://rest.ensembl.org) (keyless):
+
+- **`ensembl_list_species`** — list all species with display name, common name, assembly, taxon ID, and division
+- **`ensembl_lookup_gene`** — resolve a gene by symbol + species or by Ensembl stable ID (ENSG…)
+- **`ensembl_get_sequence`** — fetch genomic, cDNA, CDS, or protein sequence by stable ID or region string; dotted scaffold/patch names (e.g. `GL000220.1`) supported
+- **`ensembl_query_region`** — overlap features (genes, transcripts, exons, variants, regulatory) within a genomic window
+- **`ensembl_predict_variant`** — VEP consequence prediction for a variant in HGVS or `region/allele` notation
+- **`ensembl_get_homology`** — orthologs and paralogs across species via Ensembl Compara
+- **`ensembl_get_xrefs`** — external database cross-references (UniProt, RefSeq, OMIM, GO, …) for a gene or transcript
+
+## Added
+
+- **`ensembl_list_species`**, **`ensembl_lookup_gene`**, **`ensembl_get_sequence`**, **`ensembl_query_region`**, **`ensembl_predict_variant`**, **`ensembl_get_homology`**, **`ensembl_get_xrefs`** — full 7-tool surface over the Ensembl REST API
+- **`ensembl://gene/{id}`** resource — gene record by stable ID (ENSG…): location, biotype, description, transcript list
+- **`ensembl://transcript/{id}`** resource — transcript record by stable ID (ENST…): exons, translations, biotype
+- **`ensembl://species`** resource — full Ensembl species catalog
+- **`ensembl_gene_dossier`** prompt — workflow prompt to build a comprehensive gene report (lookup → sequence → homology → xrefs)
+- **`EnsemblService`** — rate-limit-aware REST client with retry, error normalization, and per-endpoint response mapping
+- **`ENSEMBL_BASE_URL`** env var — override to point at the GRCh37 endpoint (`https://grch37.rest.ensembl.org`) or a local mirror
+
+## Security
+
+- **`EnsemblService.request()`** — strips the internal request URL from `serviceUnavailable` error data; upstream URLs were previously forwarded verbatim into MCP error payloads, leaking the resolved base URL and path to clients