gene-variant-drug-nexus

name	gene_variant_drug_nexus
description	Gene-Variant-Drug Nexus - Connect gene variants to drugs: variant effect, gene-disease link, drug associations, and clinical evidence. Use this skill for translational genomics tasks involving get vep hgvs get associated targets by disease efoId get associated drugs by target name clinvar search. Combines 4 tools from 3 SCP server(s).

Gene-Variant-Drug Nexus

Discipline: Translational Genomics | Tools Used: 4 | Servers: 3

Description

Connect gene variants to drugs: variant effect, gene-disease link, drug associations, and clinical evidence.

Tools Used

• get_vep_hgvs from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_associated_targets_by_disease_efoId from opentargets-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets
• get_associated_drugs_by_target_name from opentargets-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets
• clinvar_search from search-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search

Workflow

1. Predict variant effect
2. Get disease-target associations
3. Find drugs for target
4. Check ClinVar clinical significance

Test Case

Input

{
    "hgvs": "ENSP00000269305.4:p.Arg175His",
    "disease_efo": "EFO_0000311"
}

Expected Steps

1. Predict variant effect
2. Get disease-target associations
3. Find drugs for target
4. Check ClinVar clinical significance

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 = {
    "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",
    "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)
    :  (result)

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