Biomedical APIs Server

This Model Context Protocol (MCP) server exposes 14 tools to query free biomedical and pharmaceutical APIs—plus stubs for restricted/paid sources—enabling AI agents to access clinical trial data, drug information, molecular structures, adverse events, and research literature.

---

🎯 Available APIs

Free & Open APIs (fully functional)

1. ClinicalTrials.gov → Search registered clinical trials worldwide
2. ChEMBL → Small molecules, bioactivity data, drug-like compounds
3. PubChem → Chemical compounds, molecular properties
4. OpenFDA → FDA adverse event reports (drug, device, food)
5. Europe PMC → Biomedical research articles and preprints

Restricted/Paid APIs (stubs only)

6. dbGaP → NIH genomic & clinical datasets (requires NIH credentials)
7. PhysioNet → Physiological signals (requires credentialed access)
8. MIMIC-IV → ICU records (PhysioNet credential + CITI training)
9. UK Biobank → Large-scale biomedical data (application required)
10. DrugBank → Structured drug data (academic/commercial license)
11. BindingDB → Protein-ligand binding affinities (bulk download)
12. OpenTrials → Merged trial data & sponsors (open access)
13. Crunchbase → Company & funding data (free tier limited)

---

🚀 Quick Start

1. Install Dependencies

npm install

2. Configure Environment (optional)

Copy .env.example to .env and add optional API keys:

cp .env.example .env

Edit .env:

OPENFDA_API_KEY=your_key_here  # Optional: increases OpenFDA rate limits
CRUNCHBASE_API_KEY=your_key_here  # Optional: enables Crunchbase free tier

3. Build the Server

npm run build

4. Run in Development Mode

npm run dev

5. Use in Production

npm start

---

🧪 Testing with MCP Inspector

MCP Inspector lets you test your server interactively:

npx @modelcontextprotocol/inspector node dist/server.js

Once connected, you can:

• List all 14 available tools
• Test tool calls with custom inputs
• View structured JSON responses
• Debug errors and API rate limits

---

🔌 Connecting to Clients

VS Code (Copilot Agent Mode)

The server is pre-configured in .vscode/mcp.json:

{
  "servers": {
    "biomed-apis": {
      "type": "stdio",
      "command": "node",
      "args": ["dist/server.js"]
    }
  }
}

To connect:

1. Open this workspace in VS Code
2. Restart VS Code (if needed)
3. Open Copilot Chat and confirm the MCP server is listed
4. Ask: "Search ClinicalTrials.gov for epilepsy trials started in 2023"

Claude Desktop

Add to ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "biomed-apis": {
      "command": "node",
      "args": ["C:\\For Me\\Projects\\mcp with DBs\\dist\\server.js"]
    }
  }
}

Restart Claude Desktop. The tools will appear in the MCP panel.

Claude Code CLI

claude mcp add --transport stdio biomed-apis node "C:\\For Me\\Projects\\mcp with DBs\\dist\\server.js"

---

📚 Example Tool Calls

1. Search Clinical Trials

{
  "tool": "search_clinical_trials",
  "input": {
    "query": "epilepsy",
    "filter": "AREA[StartDate]2020-01-01+TO+2023-12-31",
    "pageSize": 5
  }
}

Returns: NCT IDs, titles, status, phases, conditions, interventions

---

2. Search ChEMBL Compounds

{
  "tool": "search_chembl_compounds",
  "input": {
    "query": "aspirin",
    "limit": 5
  }
}

Returns: ChEMBL IDs, molecular formulas, weights, max clinical phase

---

3. Get ChEMBL Bioactivity Data

{
  "tool": "get_chembl_activities",
  "input": {
    "targetChemblId": "CHEMBL2",
    "limit": 10
  }
}

Returns: Activity IDs, assay IDs, molecules, types (IC50, Ki, etc.), values, units

---

4. Get PubChem Compound by Name

{
  "tool": "get_pubchem_compound",
  "input": {
    "name": "glucose"
  }
}

Returns: CID, molecular formula, weight, IUPAC name, SMILES

---

5. Search OpenFDA Drug Adverse Events

{
  "tool": "search_openfda_drug_events",
  "input": {
    "search": "patient.drug.medicinalproduct:\"metformin\"",
    "limit": 10
  }
}

Returns: Receive dates, patient ages, reactions, drug names

---

6. Search Europe PMC Articles

{
  "tool": "search_europepmc_articles",
  "input": {
    "query": "CRISPR gene editing",
    "pageSize": 10
  }
}

Returns: Article IDs, sources, titles, authors, journals, publication years

---

7. Query Restricted APIs (Stubs)

{
  "tool": "query_dbgap",
  "input": {
    "query": "GWAS cardiovascular disease"
  }
}

Returns: [dbGaP stub] Querying: "GWAS cardiovascular disease". Access requires NIH credentials & dbGaP approval.

Note: Stubs for dbGaP, PhysioNet, MIMIC-IV, UK Biobank, DrugBank, BindingDB, OpenTrials, and Crunchbase return informational messages. Replace the stub functions in src/clients/restrictedStubs.ts with real implementations once you have credentials.

---

🛠️ Project Structure

mcp-biomed-server/
├── src/
│   ├── server.ts                    # Main MCP server with all 14 tools
│   └── clients/
│       ├── clinicalTrialsClient.ts  # ClinicalTrials.gov
│       ├── chemblClient.ts          # ChEMBL
│       ├── pubchemClient.ts         # PubChem
│       ├── openfdaClient.ts         # OpenFDA
│       ├── europePmcClient.ts       # Europe PMC
│       └── restrictedStubs.ts       # Stubs for restricted APIs
├── dist/                            # Compiled JavaScript (after build)
├── .vscode/
│   └── mcp.json                     # VS Code MCP config
├── .env.example                     # Environment variable template
├── package.json
├── tsconfig.json
└── README.md

---

🔧 Development

Adding a New Tool

1. Create a client function in src/clients/ (or add to existing file)
2. Register the tool in src/server.ts:

   server.registerTool(
     'my_tool_name',
     {
       title: 'My Tool',
       description: 'What it does',
       inputSchema: { param: z.string().describe('Parameter description') },
       outputSchema: { result: z.string() }
     },
     async ({ param }) => {
       const result = await myClientFunction(param);
       return {
         content: [{ type: 'text', text: JSON.stringify({ result }) }],
         structuredContent: { result }
       };
     }
   );
   

3. Rebuild: npm run build

Debugging

• Use npm run dev for live TypeScript execution via tsx
• Server logs errors to stderr (visible in MCP Inspector or client logs)
• Check rate limits if APIs return HTTP 429

---

⚖️ Rate Limits & Best Practices

API	Rate Limit	Notes
ClinicalTrials.gov	~1000 req/day	No key required; public access
ChEMBL	Unknown (generous)	No key; community-supported
PubChem	~5 req/sec	No key; use delays for bulk requests
OpenFDA	240 req/min (1000/day without key)	API key increases to 240 req/min
Europe PMC	Unknown (generous)	No key; rate-limited

Tips:

• Use pageSize/limit parameters to control result counts
• Add exponential backoff for HTTP 429 errors
• Consider caching responses for repeated queries

---

📖 References

• Model Context Protocol Docs
• MCP TypeScript SDK
• ClinicalTrials.gov API
• ChEMBL API
• PubChem PUG REST
• OpenFDA API
• Europe PMC API

---

📝 License

MIT (adjust as needed for your project)

---

🤝 Contributing

1. Fork the repository
2. Create a feature branch (git checkout -b feature/new-api)
3. Add your client in src/clients/
4. Register tools in src/server.ts
5. Test with MCP Inspector
6. Submit a pull request

---

🐛 Troubleshooting

"Cannot find module" errors

npm install  # Reinstall dependencies
npm run build  # Rebuild after changes

VS Code doesn't recognize the MCP server

1. Ensure .vscode/mcp.json exists
2. Rebuild: npm run build
3. Restart VS Code
4. Check VS Code's MCP output panel for errors

API returns 429 (Too Many Requests)

• Add delays between requests
• Use optional API keys (OpenFDA, Crunchbase)
• Reduce pageSize/limit parameters

Stub tools return placeholder messages

• This is expected! Restricted APIs require credentials
• Replace functions in src/clients/restrictedStubs.ts with real implementations

---

🎉 Next Steps

• Test all 14 tools with MCP Inspector
• Connect to VS Code Copilot and try example queries
• Replace stubs with real API implementations (if you have access)
• Add rate limiting and caching for production use
• Extend with more APIs: BindingDB real download, OpenTrials integration, etc.

---

Built with 💙 using Model Context Protocol