ebi-search-mcp 1.0.0

package/README.md

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+# Ebi Search MCP
+
+EBI Search API: search EMBL-EBI biomedical databases. 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
+
+
+* `search`  Search a biomedical database.
+* `entry`  Get a specific entry.
+
+## Usage
+
+```bash
+npm install
+npm run build
+node dist/index.js
+```
+
+Data comes from the public Ebi Search API.

package/dist/api.js

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+const UA = 'mrfentmen-ebi-search-mcp/1.0';
+const BASE = 'https://www.ebi.ac.uk/ebisearch/ws/rest';
+export async function search(args) {
+    const size = Math.min(Math.max(Number(args?.size ?? 5) || 5, 1), 20);
+    const domain = args.domain || 'ensembl';
+    const url = `${BASE}/${encodeURIComponent(domain)}?query=${encodeURIComponent(args.query)}&size=${size}&format=json`;
+    const res = await fetch(url, {
+        headers: { 'User-Agent': UA, Accept: 'application/json' },
+        signal: AbortSignal.timeout(25000),
+    });
+    if (!res.ok)
+        throw new Error(`EBI Search returned ${res.status}`);
+    const d = (await res.json());
+    const entries = d.entries ?? [];
+    if (!entries.length)
+        return `No EBI results in "${domain}" for "${args.query}".`;
+    const lines = entries.slice(0, size).map((e, i) => {
+        const name = e.fields?.find((f) => f.name === 'name' || f.name === 'title')?.value ?? '';
+        return `${i + 1}. ${e.id ?? '?'} ${name ? `- ${name.slice(0, 80)}` : ''}`;
+    });
+    return `EBI Search "${args.query}" in ${domain} (${d.hitCount ?? entries.length} hits):\n` + lines.join('\n');
+}
+export async function entry(args) {
+    const url = `${BASE}/${encodeURIComponent(args.domain)}/entry/${encodeURIComponent(args.id)}?format=json`;
+    const res = await fetch(url, {
+        headers: { 'User-Agent': UA, Accept: 'application/json' },
+        signal: AbortSignal.timeout(25000),
+    });
+    if (!res.ok)
+        throw new Error(`EBI Search returned ${res.status}`);
+    const d = (await res.json());
+    if (!d.id)
+        throw new Error('No entry returned.');
+    const fields = (d.fields ?? []).slice(0, 15).map((f) => `* ${f.name ?? '?'}: ${(f.value ?? '').slice(0, 120)}`);
+    return `Entry ${d.id} (${d.source ?? args.domain}):\n` + fields.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 { entry } from "./api.js";
+import { search } 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: "ebi-search-mcp", version: "1.0.0" });
+    server.registerTool("search", {
+        title: "Search",
+        description: "Search a biomedical database.",
+        inputSchema: z.object({ query: z.string().describe("Search query."), domain: z.string().describe("Database domain (ensembl, uniprot, literature).").optional(), size: z.number().describe("Max results.").optional() }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        try {
+            return text(await search(args));
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
+    server.registerTool("entry", {
+        title: "Entry",
+        description: "Get a specific entry.",
+        inputSchema: z.object({ domain: z.string().describe("Database domain."), id: z.string().describe("Entry id.") }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        try {
+            return text(await entry(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/ebi-search-mcp.git"
+  },
+  "bin": {
+    "ebi-search-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": "ebi-search-mcp",
+  "description": "EBI Search API: search EMBL-EBI biomedical databases.",
+  "keywords": [
+    "mcp",
+    "ebi",
+    "search",
+    "biomedical",
+    "ensembl",
+    "uniprot"
+  ],
+  "engines": {
+    "node": ">=20"
+  },
+  "mcpName": "io.github.mrfentmen/ebi-search-mcp"
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.mrfentmen/ebi-search-mcp",
+  "description": "EBI Search API: search EMBL-EBI biomedical databases.",
+  "repository": {
+    "url": "https://github.com/mrfentmen/ebi-search-mcp",
+    "source": "github"
+  },
+  "version": "1.0.0",
+  "packages": [
+    {
+      "registryType": "npm",
+      "identifier": "ebi-search-mcp",
+      "version": "1.0.0",
+      "transport": {
+        "type": "stdio"
+      }
+    }
+  ]
+}