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Skill v1.0.1
currentAutomated scan100/100internscience/scp/gene-therapy-target
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version: "1.0.1" name: gene_therapy_target description: "Gene Therapy Target Analysis - Analyze gene therapy target: gene info, variant pathogenicity, protein structure, and clinical evidence. Use this skill for gene therapy tasks involving get gene metadata by gene name get vep hgvs Protein structure prediction ESMFold clinvar search. Combines 4 tools from 4 SCP server(s)."
Gene Therapy Target Analysis
Discipline: Gene Therapy | Tools Used: 4 | Servers: 4
Description
Analyze gene therapy target: gene info, variant pathogenicity, protein structure, and clinical evidence.
Tools Used
- `get_gene_metadata_by_gene_name` from
ncbi-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI - `get_vep_hgvs` from
ensembl-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl - `Protein_structure_prediction_ESMFold` from
server-1(sse) -https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory - `clinvar_search` from
search-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search
Workflow
- Get gene info
- Predict variant effect
- Predict protein structure
- Search ClinVar pathogenicity
Test Case
Input
json
{"gene": "CFTR","hgvs": "ENSP00000003084.6:p.Phe508del"}
Expected Steps
- Get gene info
- Predict variant effect
- Predict protein structure
- Search ClinVar pathogenicity
Usage Example
Note: Replace<YOUR_SCP_HUB_API_KEY>with your own SCP Hub API Key. You can obtain one from the SCP Platform.
python
import asyncioimport jsonfrom mcp import ClientSessionfrom mcp.client.streamable_http import streamablehttp_clientfrom mcp.client.sse import sse_clientSERVERS = {"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","server-1": "https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory","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, transportdef 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.textreturn str(result)except: return str(result)async def main():# Connect to required serverssessions = {}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["server-1"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/1/VenusFactory", "sse")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 gene inforesult_1 = await sessions["ncbi-server"].call_tool("get_gene_metadata_by_gene_name", arguments={})data_1 = parse(result_1)print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")# Step 2: Predict variant effectresult_2 = await sessions["ensembl-server"].call_tool("get_vep_hgvs", arguments={})data_2 = parse(result_2)print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")# Step 3: Predict protein structureresult_3 = await sessions["server-1"].call_tool("Protein_structure_prediction_ESMFold", arguments={})data_3 = parse(result_3)print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")# Step 4: Search ClinVar pathogenicityresult_4 = await sessions["search-server"].call_tool("clinvar_search", arguments={})data_4 = parse(result_4)print(f"Step 4 result: {json.dumps(data_4, indent=2, ensure_ascii=False)[:500]}")# Cleanupprint("Workflow complete!")if __name__ == "__main__":asyncio.run(main())