One Health Pathogen Analysis

One Health Pathogen Analysis

Discipline: One Health | Tools Used: 5 | Servers: 4

Description

One Health analysis: pathogen genome, cross-species gene comparison, antimicrobial drugs, and environmental context.

Tools Used

• get_genome_dataset_report_by_taxon from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​9/​Origene-NCBI
• get_homology_symbol from ensembl-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​12/​Origene-Ensembl
• get_mechanism_of_action_by_drug_name from fda-drug-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​14/​Origene-FDADrug
• tavily_search from search-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​7/​Origene-Search
• get_taxonomy from ncbi-server (streamable-http) - https://scp.intern-ai.org.cn/​api/​v1/​mcp/​9/​Origene-NCBI

Workflow

1. Get pathogen genome data
2. Compare virulence genes across species
3. Get antimicrobial mechanism
4. Search environmental context
5. Get taxonomy classification

Test Case

Input

{
    "taxon": "Salmonella",
    "gene": "invA",
    "drug": "ciprofloxacin"
}

Expected Steps

1. Get pathogen genome data
2. Compare virulence genes across species
3. Get antimicrobial mechanism
4. Search environmental context
5. Get taxonomy classification

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",
    "ensembl-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​12/​Origene-Ensembl",
    "fda-drug-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​14/​Origene-FDADrug",
    "search-server": "https://scp.intern-ai.org.cn/​api/​v1/​mcp/​7/​Origene-Search"
}

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")
    sessions["ensembl-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​12/​Origene-Ensembl", "streamable-http")
    sessions["fda-drug-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​14/​Origene-FDADrug", "streamable-http")
    sessions["search-server"], _, _ = await connect("https://scp.intern-ai.org.cn/​api/​v1/​mcp/​7/​Origene-Search", "streamable-http")

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

    # Step 2: Compare virulence genes across species
    result_2 = await sessions["ensembl-server"].call_tool("get_homology_symbol", arguments={})
    data_2 = parse(result_2)
    print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

    # Step 3: Get antimicrobial mechanism
    result_3 = await sessions["fda-drug-server"].call_tool("get_mechanism_of_action_by_drug_name", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

    # Step 4: Search environmental context
    result_4 = await sessions["search-server"].call_tool("tavily_search", arguments={})
    data_4 = parse(result_4)
    print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")

    # Step 5: Get taxonomy classification
    result_5 = await sessions["ncbi-server"].call_tool("get_taxonomy", arguments={})
    data_5 = parse(result_5)
    print(f"Step 5 result: {json.dumps(data_5, indent=2, ensure_ascii=False)[:500]}")

    # Cleanup
    print("Workflow complete!")

if __name__ == "__main__":
    asyncio.run(main())