@pipeworx/mcp-protein-atlas 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Pipeworx
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# mcp-protein-atlas
+
+Human Protein Atlas (HPA) MCP — keyless.
+
+Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 823+ live data sources.
+
+## Tools
+
+| Tool | Description |
+|------|-------------|
+
+## Quick Start
+
+Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
+
+```json
+{
+  "mcpServers": {
+    "protein-atlas": {
+      "url": "https://gateway.pipeworx.io/protein-atlas/mcp"
+    }
+  }
+}
+```
+
+Or connect to the full Pipeworx gateway for access to all 823+ data sources:
+
+```json
+{
+  "mcpServers": {
+    "pipeworx": {
+      "url": "https://gateway.pipeworx.io/mcp"
+    }
+  }
+}
+```
+
+## Using with ask_pipeworx
+
+Instead of calling tools directly, you can ask questions in plain English:
+
+```
+ask_pipeworx({ question: "your question about Protein Atlas data" })
+```
+
+The gateway picks the right tool and fills the arguments automatically.
+
+## More
+
+- [All tools and guides](https://github.com/pipeworx-io/examples)
+- [pipeworx.io](https://pipeworx.io)
+
+## License
+
+MIT

package/package.json

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+{
+  "name": "@pipeworx/mcp-protein-atlas",
+  "version": "0.1.0",
+  "description": "Human Protein Atlas (HPA) MCP — keyless.",
+  "type": "module",
+  "main": "src/index.ts",
+  "types": "src/index.ts",
+  "keywords": ["mcp", "mcp-server", "model-context-protocol", "pipeworx", "protein-atlas"],
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/pipeworx-io/mcp-protein-atlas"
+  },
+  "scripts": {
+    "typecheck": "tsc --noEmit"
+  },
+  "devDependencies": {
+    "typescript": "^5.7.0"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.pipeworx-io/protein-atlas",
+  "title": "Protein Atlas",
+  "description": "Human Protein Atlas (HPA) MCP — keyless.",
+  "version": "0.1.0",
+  "websiteUrl": "https://pipeworx.io/packs/protein-atlas",
+  "repository": {
+    "url": "https://github.com/pipeworx-io/mcp-protein-atlas",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gateway.pipeworx.io/protein-atlas/mcp"
+    }
+  ]
+}

package/src/index.ts

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+interface McpToolDefinition {
+  name: string;
+  description: string;
+  inputSchema: {
+    type: 'object';
+    properties: Record<string, unknown>;
+    required?: string[];
+  };
+}
+
+interface McpToolExport {
+  tools: McpToolDefinition[];
+  callTool: (name: string, args: Record<string, unknown>) => Promise<unknown>;
+  meter?: { credits: number };
+  cost?: Record<string, unknown>;
+  provider?: string;
+}
+
+/**
+ * Human Protein Atlas (HPA) MCP — keyless.
+ *
+ * Expression & localization atlas for human proteins: search genes, get a
+ * protein's tissue/cell expression, subcellular localization, protein class,
+ * and disease involvement, or list its top-expressing tissues by RNA nTPM.
+ * Use Ensembl gene ids (search_genes returns them).
+ */
+
+
+const BASE = 'https://www.proteinatlas.org';
+const UA = 'pipeworx/1.0 (+https://pipeworx.io)';
+
+const tools: McpToolExport['tools'] = [
+  {
+    name: 'search_genes',
+    description:
+      'Search the Human Protein Atlas for human genes/proteins by gene symbol or keyword. Returns each gene with its Ensembl gene id (needed by get_protein and top_tissues), synonyms, and description. Keyless.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        query: { type: 'string', description: 'Gene symbol (e.g. "EGFR") or keyword (e.g. "insulin receptor").' },
+        limit: { type: 'number', description: 'Max genes to return (default 15).' },
+      },
+      required: ['query'],
+    },
+  },
+  {
+    name: 'get_protein',
+    description:
+      "Get a trimmed Human Protein Atlas profile for one protein by Ensembl gene id (e.g. \"ENSG00000146648\"): gene, description, protein class, biological process, molecular function, RNA tissue specificity/distribution, subcellular location, and disease involvement. Use search_genes to find the Ensembl id. Keyless.",
+    inputSchema: {
+      type: 'object',
+      properties: {
+        ensembl_id: { type: 'string', description: 'An Ensembl gene id like "ENSG00000146648".' },
+      },
+      required: ['ensembl_id'],
+    },
+  },
+  {
+    name: 'top_tissues',
+    description:
+      'List a protein\'s top-expressing human tissues by RNA expression (nTPM), highest first, for one Ensembl gene id. Use search_genes to find the Ensembl id. Keyless.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        ensembl_id: { type: 'string', description: 'An Ensembl gene id like "ENSG00000146648".' },
+        limit: { type: 'number', description: 'Max tissues to return (default 10).' },
+      },
+      required: ['ensembl_id'],
+    },
+  },
+];
+
+async function callTool(name: string, args: Record<string, unknown>): Promise<unknown> {
+  try {
+    switch (name) {
+      case 'search_genes':
+        return await searchGenes(args);
+      case 'get_protein':
+        return await getProtein(args);
+      case 'top_tissues':
+        return await topTissues(args);
+      default:
+        return { error: `Unknown tool: ${name}` };
+    }
+  } catch (err) {
+    return { error: err instanceof Error ? err.message : String(err) };
+  }
+}
+
+async function searchGenes(args: Record<string, unknown>): Promise<unknown> {
+  const query = reqStr(args, 'query');
+  const limit = numArg(args.limit, 15);
+  const url = `${BASE}/api/search_download.php?search=${encodeURIComponent(query)}&format=json&columns=g,gs,eg,gd&compress=no`;
+  const data = await fetchJson(url);
+  const rows = Array.isArray(data) ? data : [];
+  const genes = rows.slice(0, limit).map((g: any) => ({
+    gene: g.Gene,
+    ensembl: g.Ensembl,
+    synonyms: g['Gene synonym'],
+    description: g['Gene description'],
+  }));
+  return { count: genes.length, genes };
+}
+
+async function getProtein(args: Record<string, unknown>): Promise<unknown> {
+  const ensemblId = reqStr(args, 'ensembl_id');
+  const url = `${BASE}/${encodeURIComponent(ensemblId)}.json`;
+  let d: any;
+  try {
+    d = await fetchJson(url);
+  } catch {
+    return { error: 'protein not found', ensembl_id: ensemblId };
+  }
+  if (!d || typeof d !== 'object') return { error: 'protein not found', ensembl_id: ensemblId };
+  return {
+    gene: d.Gene,
+    ensembl: d.Ensembl,
+    description: d['Gene description'],
+    protein_class: d['Protein class'],
+    biological_process: d['Biological process'],
+    molecular_function: d['Molecular function'],
+    rna_tissue_specificity: d['RNA tissue specificity'],
+    rna_tissue_distribution: d['RNA tissue distribution'],
+    subcellular_location: d['Subcellular main location'] ?? d['Subcellular location'],
+    disease_involvement: d['Disease involvement'],
+  };
+}
+
+async function topTissues(args: Record<string, unknown>): Promise<unknown> {
+  const ensemblId = reqStr(args, 'ensembl_id');
+  const limit = numArg(args.limit, 10);
+  const url = `${BASE}/${encodeURIComponent(ensemblId)}.json`;
+  let d: any;
+  try {
+    d = await fetchJson(url);
+  } catch {
+    return { ensembl_id: ensemblId, tissues: [] };
+  }
+  const ntpm = d?.['RNA tissue specific nTPM'];
+  if (!ntpm || typeof ntpm !== 'object') return { ensembl_id: ensemblId, tissues: [] };
+  const tissues = Object.entries(ntpm as Record<string, unknown>)
+    .map(([tissue, value]) => ({ tissue, nTPM: Number(value) }))
+    .sort((a, b) => b.nTPM - a.nTPM)
+    .slice(0, limit);
+  return { ensembl_id: ensemblId, gene: d.Gene, tissues };
+}
+
+async function fetchJson(url: string): Promise<unknown> {
+  const res = await fetch(url, { headers: { Accept: 'application/json', 'User-Agent': UA } });
+  if (!res.ok) throw new Error(`HPA: ${res.status} ${await res.text().then((t) => t.slice(0, 200))}`);
+  return res.json();
+}
+
+function reqStr(args: Record<string, unknown>, key: string): string {
+  const v = args[key];
+  if (typeof v !== 'string' || !v.trim()) throw new Error(`Required argument "${key}" is missing.`);
+  return v;
+}
+
+function numArg(v: unknown, fallback: number): number {
+  const n = typeof v === 'number' ? v : typeof v === 'string' ? Number(v) : NaN;
+  return Number.isFinite(n) && n > 0 ? Math.floor(n) : fallback;
+}
+
+export default { tools, callTool, meter: { credits: 1 } } satisfies McpToolExport;

package/tsconfig.json

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+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "ESNext",
+    "moduleResolution": "bundler",
+    "strict": true,
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+    "outDir": "dist",
+    "rootDir": "src",
+    "declaration": true
+  },
+  "include": ["src"]
+}