rare_disease_genetics: Скилл анализа генетики редких болезней

--- name: rare_disease_genetics description: "Rare Disease Genetic Analysis - Analyze rare disease genetics: Monarch phenotype-disease mapping, ClinVar variants, NCBI gene data, and OpenTargets. Use this skill for rare disease genetics tasks involving get HPO ID by phenotype get joint associated diseases by HPO ID list clinvar search get associated targets by disease efoId. Combines 4 tools from 3 SCP server(s)." --- # Rare Disease Genetic Analysis **Discipline**: Rare Disease Genetics | **Tools Used**: 4 | **Servers**: 3 ## Description Analyze rare disease genetics: Monarch phenotype-disease mapping, ClinVar variants, NCBI gene data, and OpenTargets. ## Tools Used - **`get_HPO_ID_by_phenotype`** from `monarch-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch` - **`get_joint_associated_diseases_by_HPO_ID_list`** from `monarch-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch` - **`clinvar_search`** from `search-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search` - **`get_associated_targets_by_disease_efoId`** from `opentargets-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets` ## Workflow 1. Get HPO ID for phenotype 2. Find associated diseases 3. Search ClinVar for pathogenic variants 4. Get OpenTargets target associations ## Test Case ### Input ```json { "phenotype": "seizures", "hpo_ids": [ "HP:0001250" ] } ``` ### Expected Steps 1. Get HPO ID for phenotype 2. Find associated diseases 3. Search ClinVar for pathogenic variants 4. Get OpenTargets target associations ## 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 = { "monarch-server": "https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch", "search-server": "https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", "opentargets-server": "https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets" } 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["monarch-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/16/Origene-Monarch", stack) sessions["search-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", stack) sessions["opentargets-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets", stack) # Execute workflow steps # Step 1: Get HPO ID for phenotype result_1 = await sessions["monarch-server"].call_tool("get_HPO_ID_by_phenotype", arguments={}) data_1 = parse(result_1) print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}") # Step 2: Find associated diseases result_2 = await sessions["monarch-server"].call_tool("get_joint_associated_diseases_by_HPO_ID_list", arguments={}) data_2 = parse(result_2) print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}") # Step 3: Search ClinVar for pathogenic variants result_3 = await sessions["search-server"].call_tool("clinvar_search", arguments={}) data_3 = parse(result_3) print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}") # Step 4: Get OpenTargets target associations result_4 = await sessions["opentargets-server"].call_tool("get_associated_targets_by_disease_efoId", 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()) ```