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compound_database_crossref

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Cross-Database Compound Lookup - Cross-reference compound across databases: PubChem, ChEMBL, KEGG, and CAS number lookup. Use this skill for chemical information tasks involving get compound by name get molecule by name kegg find CASToPrice. Combines 4 tools from 4 SCP server(s).

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Cross-Database Compound Lookup

Discipline: Chemical Information | Tools Used: 4 | Servers: 4

Description

Cross-reference compound across databases: PubChem, ChEMBL, KEGG, and CAS number lookup.

Tools Used

  • get_compound_by_name from pubchem-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem
  • get_molecule_by_name from chembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL
  • kegg_find from kegg-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG
  • CASToPrice from server-30 (sse) - https://scp.intern-ai.org.cn/api/v1/mcp/30/SciToolAgent-Mat

Workflow

  1. Get PubChem entry
  2. Get ChEMBL molecule entry
  3. Search KEGG
  4. Look up CAS number and pricing

Test Case

Input

{
    "compound_name": "aspirin"
}

Expected Steps

  1. Get PubChem entry
  2. Get ChEMBL molecule entry
  3. Search KEGG
  4. Look up CAS number and pricing

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 = {
    "pubchem-server": "https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem",
    "chembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL",
    "kegg-server": "https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG",
    "server-30": "https://scp.intern-ai.org.cn/api/v1/mcp/30/SciToolAgent-Mat"
}

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)

async def main():
    async with AsyncExitStack() as stack:
        # Connect to required servers
        sessions = {}
        sessions["pubchem-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/8/Origene-PubChem", stack)
        sessions["chembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL", stack)
        sessions["kegg-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG", stack)
        sessions["server-30"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/30/SciToolAgent-Mat", stack)

        # Execute workflow steps
        # Step 1: Get PubChem entry
        result_1 = await sessions["pubchem-server"].call_tool("get_compound_by_name", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Get ChEMBL molecule entry
        result_2 = await sessions["chembl-server"].call_tool("get_molecule_by_name", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Search KEGG
        result_3 = await sessions["kegg-server"].call_tool("kegg_find", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Look up CAS number and pricing
        result_4 = await sessions["server-30"].call_tool("CASToPrice", 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())