Gene-Disease Association Analysis

Gene-Disease Association Analysis

Discipline: Medical Genetics | Tools Used: 4 | Servers: 4

Description

Analyze gene-disease associations: NCBI gene metadata, OpenTargets disease associations, TCGA expression, and Monarch phenotypes.

Tools Used

• get_gene_metadata_by_gene_name from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​9/​Origene-NCBI
• get_associated_targets_by_disease_efoId from opentargets-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​15/​Origene-OpenTargets
• get_gene_expression_across_cancers from tcga-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​11/​Origene-TCGA
• get_joint_associated_diseases_by_HPO_ID_list from monarch-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​16/​Origene-Monarch

Workflow

1. Get gene metadata from NCBI
2. Get disease-target associations from OpenTargets
3. Analyze TCGA cancer expression
4. Check Monarch disease associations

Test Case

Input

{
    "gene_name": "TP53",
    "disease_efo": "EFO_0000311"
}

Expected Steps

1. Get gene metadata from NCBI
2. Get disease-target associations from OpenTargets
3. Analyze TCGA cancer expression
4. Check Monarch disease associations

Usage Example

Note: Replace <YOUR_SCP_HUB_API_KEY> with your own SCP Hub API Key. You can obtain one from the SCP Platform.

import asyncio
import json
from mcp import ClientSession
from mcp.client.streamable_http import streamablehttp_client
from mcp.client.sse import sse_client

SERVERS = {
    "ncbi-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​9/​Origene-NCBI",
    "opentargets-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​15/​Origene-OpenTargets",
    "tcga-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​11/​Origene-TCGA",
    "monarch-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​16/​Origene-Monarch"
}

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["ncbi-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​9/​Origene-NCBI", "streamable-http")
    sessions["opentargets-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​15/​Origene-OpenTargets", "streamable-http")
    sessions["tcga-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​11/​Origene-TCGA", "streamable-http")
    sessions["monarch-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​16/​Origene-Monarch", "streamable-http")

    # Execute workflow steps
    # Step 1: Get gene metadata from NCBI
    result_1 = await sessions["ncbi-server"].call_tool("get_gene_metadata_by_gene_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 disease-target associations from OpenTargets
    result_2 = await sessions["opentargets-server"].call_tool("get_associated_targets_by_disease_efoId", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

    # Step 3: Analyze TCGA cancer expression
    result_3 = await sessions["tcga-server"].call_tool("get_gene_expression_across_cancers", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

    # Step 4: Check Monarch disease associations
    result_4 = await sessions["monarch-server"].call_tool("get_joint_associated_diseases_by_HPO_ID_list", 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())