SpectrAI-Initiative/rare_disease_genetics

Rare Disease Genetic Analysis

Discipline: Rare Disease Genetics | Tools Used: 4 | Servers: 3

Description

Analyze rare disease genetics: Monarch phenotype-disease mapping, ClinVar variants, NCBI gene data, and OpenTargets.

Tools Used

• get_HPO_ID_by_phenotype from monarch-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch
• 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
• clinvar_search from search-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search
• get_associated_targets_by_disease_efoId from opentargets-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets

Workflow

1. Get HPO ID for phenotype
2. Find associated diseases
3. Search ClinVar for pathogenic variants
4. Get OpenTargets target associations

Test Case

Input

{
    "phenotype": "seizures",
    "hpo_ids": [
        "HP:0001250"
    ]
}

Expected Steps

1. Get HPO ID for phenotype
2. Find associated diseases
3. Search ClinVar for pathogenic variants
4. Get OpenTargets target associations

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 = {
    "monarch-server": "https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch",
    "search-server": "https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search",
    "opentargets-server": "https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets"
}

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["monarch-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch", stack)
        sessions["search-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", stack)
        sessions["opentargets-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets", stack)

        # Execute workflow steps
        # Step 1: Get HPO ID for phenotype
        result_1 = await sessions["monarch-server"].call_tool("get_HPO_ID_by_phenotype", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Find associated diseases
        result_2 = await sessions["monarch-server"].call_tool("get_joint_associated_diseases_by_HPO_ID_list", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Search ClinVar for pathogenic variants
        result_3 = await sessions["search-server"].call_tool("clinvar_search", arguments={})
        data_3 = parse(result_3)
        print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

        # Step 4: Get OpenTargets target associations
        result_4 = await sessions["opentargets-server"].call_tool("get_associated_targets_by_disease_efoId", 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())