lab-protocol-from-literature

name	lab_protocol_from_literature
description	Lab Protocol from Literature - Extract and generate lab protocol: search PubMed, extract protocol from paper, and generate executable protocol. Use this skill for lab science tasks involving pubmed search extract protocol from pdf protocol generation generate executable json. Combines 4 tools from 2 SCP server(s).

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

{
    "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 sk-b04409a1-b32b-4511-9aeb-22980abdc05c with your own SCP Hub API Key. You can obtain one from the SCP Platform.

import asyncio
import json
from contextlib import AsyncExitStack
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, stack):
    transport = streamablehttp_client(url=url, headers={"SCP-HUB-API-KEY": "sk-b04409a1-b32b-4511-9aeb-22980abdc05c"})
    read, write, _ = await stack.enter_async_context(transport)
    ctx = ClientSession(read, write)
    session = await stack.enter_async_context(ctx)
    await session.initialize()
    return session

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)

  ():
      AsyncExitStack()  stack:
        
        sessions = {}
        sessions[] =  connect(, stack)
        sessions[] =  connect(, stack)

        
        
        result_1 =  sessions[].call_tool(, arguments={})
        data_1 = parse(result_1)
        ()

        
        result_2 =  sessions[].call_tool(, arguments={})
        data_2 = parse(result_2)
        ()

        
        result_3 =  sessions[].call_tool(, arguments={})
        data_3 = parse(result_3)
        ()

        
        result_4 =  sessions[].call_tool(, arguments={})
        data_4 = parse(result_4)
        ()

        
        ()

 __name__ == :
    asyncio.run(main())