gene-comprehensive-lookup

name	gene_comprehensive_lookup
description	Gene Comprehensive Lookup - Comprehensive gene lookup: NCBI gene data, Ensembl gene info, UniProt protein data, and KEGG pathway links. Use this skill for bioinformatics tasks involving get gene metadata by gene name get lookup symbol get general info by protein or gene name kegg find. Combines 4 tools from 4 SCP server(s).

Gene Comprehensive Lookup

Discipline: Bioinformatics | Tools Used: 4 | Servers: 4

Description

Comprehensive gene lookup: NCBI gene data, Ensembl gene info, UniProt protein data, and KEGG pathway links.

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_lookup_symbol from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_general_info_by_protein_or_gene_name from uniprot-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt
• kegg_find from kegg-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG

Workflow

1. Get NCBI gene metadata
2. Look up in Ensembl
3. Get UniProt protein info
4. Find in KEGG

Test Case

Input

{
    "gene_name": "BRCA1",
    "species": "homo_sapiens"
}

Expected Steps

1. Get NCBI gene metadata
2. Look up in Ensembl
3. Get UniProt protein info
4. Find in KEGG

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 = {
    "ncbi-server": "https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI",
    "ensembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl",
    "uniprot-server": "https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt",
    "kegg-server": "https://scp.intern-ai.org.cn/api/v1/mcp/5/Origene-KEGG"
}

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:  c.text
         (result)
    :  (result)

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