epigenomic-landscape

name	epigenomic_landscape
description	Epigenomic Landscape Mapping - Map epigenomic landscape: overlapping features, regulatory elements, binding matrices, and phenotype links. Use this skill for epigenomics tasks involving get overlap region get phenotype region get species binding matrix get track data. Combines 4 tools from 2 SCP server(s).

Epigenomic Landscape Mapping

Discipline: Epigenomics | Tools Used: 4 | Servers: 2

Description

Map epigenomic landscape: overlapping features, regulatory elements, binding matrices, and phenotype links.

Tools Used

• get_overlap_region from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_phenotype_region from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_species_binding_matrix from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl
• get_track_data from ucsc-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC

Workflow

1. Get overlapping regulatory features
2. Get phenotype associations in region
3. Get binding matrix data
4. Get UCSC epigenomic track data

Test Case

Input

{
    "region": "17:43044295-43125370",
    "species": "homo_sapiens",
    "genome": "hg38"
}

Expected Steps

1. Get overlapping regulatory features
2. Get phenotype associations in region
3. Get binding matrix data
4. Get UCSC epigenomic track data

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 = {
    "ensembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl",
    "ucsc-server": "https://scp.intern-ai.org.cn/api/v1/mcp/13/Origene-UCSC"
}

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():
    
    sessions = {}
    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())