multiomics-integration

name	multiomics_integration
description	Multi-Omics Integration - Integrate multi-omics: gene expression, protein data, pathway enrichment, and metabolic pathways. Use this skill for multi-omics tasks involving get gene expression across cancers get uniprotkb entry by accession get functional enrichment kegg get. Combines 4 tools from 4 SCP server(s).

Multi-Omics Integration

Discipline: Multi-Omics | Tools Used: 4 | Servers: 4

Description

Integrate multi-omics: gene expression, protein data, pathway enrichment, and metabolic pathways.

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_uniprotkb_entry_by_accession from uniprot-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt
• get_functional_enrichment from string-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/6/Origene-STRING
• kegg_get from kegg-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG

Workflow

1. Get transcriptomic data
2. Get proteomic data
3. Run pathway enrichment
4. Get metabolic pathway details

Test Case

Input

{
    "gene": "TP53",
    "accession": "P04637",
    "pathway": "hsa04115"
}

Expected Steps

1. Get transcriptomic data
2. Get proteomic data
3. Run pathway enrichment
4. Get metabolic pathway details

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 = {
    "tcga-server": "https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA",
    "uniprot-server": "https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt",
    "string-server": "https://scp.intern-ai.org.cn/api/v1/mcp/6/Origene-STRING",
    "kegg-server": "https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG"
}

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)
    :  (result)

  ():
    
    sessions = {}
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )
    sessions[], _, _ =  connect(, )

    
    
    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())