lab-protocol-from-literature

# Lab Protocol from Literature **Discipline**: Lab Science | **Tools Used**: 4 | **Servers**: 2 ## Description Extract and generate lab protocol: search PubMed, extract protocol from paper, and generate executable protocol. ## Tools Used - **`pubmed_search`** from `search-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search` - **`extract_protocol_from_pdf`** from `server-19` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan` - **`protocol_generation`** from `server-19` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan` - **`generate_executable_json`** from `server-19` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan` ## Workflow 1. Search PubMed for protocols 2. Extract protocol from paper 3. Generate standard protocol 4. Create executable JSON ## Test Case ### Input ```json { "query": "PCR amplification protocol for BRCA1" } ``` ### Expected Steps 1. Search PubMed for protocols 2. Extract protocol from paper 3. Generate standard protocol 4. Create executable JSON ## Usage Example > **Note:** Replace `<YOUR_SCP_HUB_API_KEY>` with your own SCP Hub API Key. You can obtain one from the [SCP Platform](https://scphub.intern-ai.org.cn). ```python import asyncio import json from mcp import ClientSession from mcp.client.streamable_http import streamablehttp_client from mcp.client.sse import sse_client SERVERS = { "search-server": "https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", "server-19": "https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan" } async def connect(url, transport_type): transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "<YOUR_SCP_HUB_API_KEY>"}) read, write, _ = await transport.__aenter__() ctx = ClientSession(read, write) session = await ctx.__aenter__() await session.initialize() return session, ctx, transport def parse(result): try: if hasattr(result, 'content') and result.content: c = result.content[0] if hasattr(c, 'text'): try: return json.loads(c.text) except: return c.text return str(result) except: return str(result) async def main(): # Connect to required servers sessions = {} sessions["search-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", "streamable-http") sessions["server-19"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/19/Thoth-Plan", "streamable-http") # Execute workflow steps # Step 1: Search PubMed for protocols result_1 = await sessions["search-server"].call_tool("pubmed_search", arguments={}) data_1 = parse(result_1) print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}") # Step 2: Extract protocol from paper result_2 = await sessions["server-19"].call_tool("extract_protocol_from_pdf", arguments={}) data_2 = parse(result_2) print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}") # Step 3: Generate standard protocol result_3 = await sessions["server-19"].call_tool("protocol_generation", arguments={}) data_3 = parse(result_3) print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}") # Step 4: Create executable JSON result_4 = await sessions["server-19"].call_tool("generate_executable_json", arguments={}) data_4 = parse(result_4) print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}") # Cleanup print("Workflow complete!") if __name__ == "__main__": asyncio.run(main()) ```