ensembl-mcp 1.0.0

package/README.md

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+# Ensembl MCP
+
+Genome data from the public Ensembl REST API. No key required.
+
+This file is self contained. It reads public data only and never writes to the machine. All output is bounded and honest about what could not be fetched.
+
+## Tools
+
+
+* `lookup`  Look up a gene.
+* `sequence`  Get a sequence.
+
+## Usage
+
+```bash
+npm install
+npm run build
+node dist/index.js
+```
+
+Data comes from the public Ensembl REST API.

package/dist/api.js

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+const BASE = 'https://rest.ensembl.org';
+export async function lookup(args) {
+    const symbol = (args.symbol ?? '').trim();
+    const species = (args.species ?? 'human').trim();
+    if (!symbol)
+        return 'Provide a gene symbol.';
+    const res = await fetch(`${BASE}/lookup/symbol/${encodeURIComponent(species)}/${encodeURIComponent(symbol)}?content-type=application/json`, {
+        headers: { 'User-Agent': 'mrfentmen-ensembl-mcp/1.0', Accept: 'application/json' },
+        signal: AbortSignal.timeout(20000),
+    });
+    if (!res.ok)
+        throw new Error(`Ensembl returned ${res.status}`);
+    const d = (await res.json());
+    const s = (k) => (d[k] != null ? String(d[k]) : '');
+    return [
+        `${s('display_name')} (${s('id')})`,
+        s('description') ? `Description: ${s('description')}` : '',
+        `Type: ${s('biotype')} | ${s('start')}-${s('end')} on ${s('seq_region_name')} (${s('strand') === '1' ? '+' : '-'})`,
+        s('assembly_name') ? `Assembly: ${s('assembly_name')}` : '',
+    ].filter(Boolean).join('\n');
+}
+export async function sequence(args) {
+    const id = (args.id ?? '').trim();
+    if (!id)
+        return 'Provide a stable id.';
+    const res = await fetch(`${BASE}/sequence/id/${encodeURIComponent(id)}?content-type=application/json`, {
+        headers: { 'User-Agent': 'mrfentmen-ensembl-mcp/1.0', Accept: 'application/json' },
+        signal: AbortSignal.timeout(20000),
+    });
+    if (!res.ok)
+        throw new Error(`Ensembl returned ${res.status}`);
+    const d = (await res.json());
+    const seq = String(d.seq ?? '');
+    return [
+        `Sequence for ${id} (${seq.length} bases):`,
+        seq.slice(0, 200) + (seq.length > 200 ? '...' : ''),
+    ].filter(Boolean).join('\n');
+}

package/dist/index.js

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+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { createServer } from "./server.js";
+const main = async () => { const server = createServer(); await server.connect(new StdioServerTransport()); };
+main().catch((error) => { console.error("Fatal error:", error); process.exit(1); });

package/dist/server.js

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+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { z } from "zod";
+import { lookup } from "./api.js";
+import { sequence } from "./api.js";
+const text = (value) => ({ content: [{ type: "text", text: value }] });
+const textError = (t) => ({ content: [{ type: "text", text: t }], isError: true });
+const READ_ONLY = { readOnlyHint: true, openWorldHint: true };
+const error = (e) => `Error: ${e instanceof Error ? e.message : String(e)}`;
+export function createServer() {
+    const server = new McpServer({ name: "ensembl-mcp", version: "1.0.0" });
+    server.registerTool("lookup", {
+        title: "Lookup",
+        description: "Look up a gene symbol.",
+        inputSchema: z.object({ species: z.string().describe("Species, e.g. human.").optional(), symbol: z.string().describe("Gene symbol.") }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        try {
+            return text(await lookup(args));
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
+    server.registerTool("sequence", {
+        title: "Sequence",
+        description: "Get sequence for a stable id.",
+        inputSchema: z.object({ id: z.string().describe("Stable transcript id.") }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        try {
+            return text(await sequence(args));
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
+    return server;
+}

package/package.json

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+{
+  "version": "1.0.0",
+  "type": "module",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/mrfentmen/ensembl-mcp.git"
+  },
+  "bin": {
+    "ensembl-mcp": "./dist/index.js"
+  },
+  "main": "./dist/index.js",
+  "files": [
+    "dist",
+    "server.json",
+    "README.md"
+  ],
+  "scripts": {
+    "build": "tsc -p tsconfig.json",
+    "start": "node dist/index.js",
+    "dev": "npm run build && node dist/index.js"
+  },
+  "license": "MIT",
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.0.4",
+    "zod": "^3.23.8"
+  },
+  "devDependencies": {
+    "@types/node": "^22.0.0",
+    "typescript": "^5.6.0"
+  },
+  "name": "ensembl-mcp",
+  "description": "Genome lookup from Ensembl. No key required.",
+  "mcpName": "io.github.mrfentmen/ensembl-mcp",
+  "keywords": [
+    "mcp",
+    "ensembl",
+    "genome",
+    "genes",
+    "bioinformatics"
+  ],
+  "engines": {
+    "node": ">=20"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.mrfentmen/ensembl-mcp",
+  "description": "Genome lookup from Ensembl. No key required.",
+  "repository": {
+    "url": "https://github.com/mrfentmen/ensembl-mcp",
+    "source": "github"
+  },
+  "version": "1.0.0",
+  "packages": [
+    {
+      "registryType": "npm",
+      "identifier": "ensembl-mcp",
+      "version": "1.0.0",
+      "transport": {
+        "type": "stdio"
+      }
+    }
+  ]
+}