--- name: rare-disease-genetics-5eb39140af09 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()) ``` --- Source attribution: SpectrAI-Initiative Original project: https://github.com/SpectrAI-Initiative/InnoClaw License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Dave AI. ## Upstream license notice MIT License Copyright (c) 2026 Gabriel Moreira Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Dave AI resource metadata Creator / publisher: SpectrAI-Initiative Original project: https://github.com/SpectrAI-Initiative/InnoClaw Attribution basis: Upstream repository explicitly recorded in package mirror path Fields of work: Education & Research, Healthcare & Life Sciences Roles: Clinical Research, Health Informatics, Researcher Specialties: API Tools: Monarch Server, Opentargets Server, Search Server Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: c7ff1b3df30fb34ef2b4e5d61992c60f0d4e4222a8ea29f8dcf438352f36e1b4