Biosample Genomics

BioSample & Genome Cross-Reference

Discipline: Genomics | Tools Used: 4 | Servers: 1

Description

Cross-reference biosample and genome data: NCBI biosample, genome report, sequence reports, and taxonomy.

Tools Used

• get_biosample_report from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI
• get_genome_dataset_report_by_accession from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI
• get_genome_sequence_reports from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI
• get_taxonomy from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI

Workflow

1. Get biosample report
2. Get genome dataset report
3. Get sequence reports
4. Get taxonomy

Test Case

Input

{
    "biosample": "SAMN15795254",
    "genome_accession": "GCF_000001405.40"
}

Expected Steps

1. Get biosample report
2. Get genome dataset report
3. Get sequence reports
4. Get taxonomy

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 = {
    "ncbi-server": "https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI"
}

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():
    # Connect to required servers
    sessions = {}
    sessions["ncbi-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI", "streamable-http")

    # Execute workflow steps
    # Step 1: Get biosample report
    result_1 = await sessions["ncbi-server"].call_tool("get_biosample_report", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

    # Step 2: Get genome dataset report
    result_2 = await sessions["ncbi-server"].call_tool("get_genome_dataset_report_by_accession", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

    # Step 3: Get sequence reports
    result_3 = await sessions["ncbi-server"].call_tool("get_genome_sequence_reports", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

    # Step 4: Get taxonomy
    result_4 = await sessions["ncbi-server"].call_tool("get_taxonomy", 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())