biosample_genomics: Скилл для анализа геномных данных

--- name: biosample_genomics description: "BioSample & Genome Cross-Reference - Cross-reference biosample and genome data: NCBI biosample, genome report, sequence reports, and taxonomy. Use this skill for genomics tasks involving get biosample report get genome dataset report by accession get genome sequence reports get taxonomy. Combines 4 tools from 1 SCP server(s)." --- # 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 ```json { "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 `sk-b04409a1-b32b-4511-9aeb-22980abdc05c` with your own SCP Hub API Key. You can obtain one from the [SCP Platform](https://scphub.intern-ai.org.cn). ```python 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" } 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: return c.text return str(result) except: return str(result) async def main(): async with AsyncExitStack() as stack: # Connect to required servers sessions = {} sessions["ncbi-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI", stack) # 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()) ```