Precision Oncology Workflow

Discipline: Precision Oncology | Tools Used: 5 | Servers: 5

Description

Precision oncology: tumor expression profiling, variant analysis, targeted therapy lookup, and clinical trials.

Tools Used

• get_gene_expression_across_cancers from tcga-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA
• get_vep_hgvs from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_associated_drugs_by_target_name from opentargets-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets
• get_clinical_studies_info_by_drug_name from fda-drug-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/14/Origene-FDADrug
• pubmed_search from search-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search

Workflow

1. Profile tumor gene expression
2. Analyze driver mutation
3. Find targeted therapies
4. Get clinical trial data
5. Search clinical evidence

Test Case

Input

{
    "gene": "BRAF",
    "variant": "ENSP00000288602.7:p.Val600Glu",
    "drug": "vemurafenib"
}

Expected Steps

1. Profile tumor gene expression
2. Analyze driver mutation
3. Find targeted therapies
4. Get clinical trial data
5. Search clinical evidence

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 = {
    "tcga-server": "https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA",
    "ensembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl",
    "opentargets-server": "https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets",
    "fda-drug-server": "https://scp.intern-ai.org.cn/api/v1/mcp/14/Origene-FDADrug",
    "search-server": "https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search"
}

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["tcga-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA", stack)
        sessions["ensembl-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl", stack)
        sessions["opentargets-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets", stack)
        sessions["fda-drug-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/14/Origene-FDADrug", stack)
        sessions["search-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", stack)

        # Execute workflow steps
        # Step 1: Profile tumor gene expression
        result_1 = await sessions["tcga-server"].call_tool("get_gene_expression_across_cancers", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Analyze driver mutation
        result_2 = await sessions["ensembl-server"].call_tool("get_vep_hgvs", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Find targeted therapies
        result_3 = await sessions["opentargets-server"].call_tool("get_associated_drugs_by_target_name", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Get clinical trial data
        result_4 = await sessions["fda-drug-server"].call_tool("get_clinical_studies_info_by_drug_name", arguments={})
        data_4 = parse(result_4)
        print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

        # Step 5: Search clinical evidence
        result_5 = await sessions["search-server"].call_tool("pubmed_search", arguments={})
        data_5 = parse(result_5)
        print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")

        # Cleanup
        print("Workflow complete!")

if __name__ == "__main__":
    asyncio.run(main())