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Skill v1.0.1
currentAutomated scan100/100internscience/scp/organism-classification
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version: "1.0.1" name: organism_classification description: "Organism Classification & Database - Classify organism: NCBI taxonomy, Ensembl taxonomy, ChEMBL organisms, and genome info. Use this skill for taxonomy tasks involving get taxonomy get taxonomy id get organism by id get genome dataset report by taxon. Combines 4 tools from 3 SCP server(s)."
Organism Classification & Database
Discipline: Taxonomy | Tools Used: 4 | Servers: 3
Description
Classify organism: NCBI taxonomy, Ensembl taxonomy, ChEMBL organisms, and genome info.
Tools Used
- `get_taxonomy` from
ncbi-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI - `get_taxonomy_id` from
ensembl-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl - `get_organism_by_id` from
chembl-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL - `get_genome_dataset_report_by_taxon` from
ncbi-server(streamable-http) -https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI
Workflow
- Get NCBI taxonomy
- Get Ensembl taxonomy
- Get ChEMBL organism info
- Get genome dataset report
Test Case
Input
json
{"taxon": "9606","species": "homo_sapiens"}
Expected Steps
- Get NCBI taxonomy
- Get Ensembl taxonomy
- Get ChEMBL organism info
- Get genome dataset report
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","chembl-server": "https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL"}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["chembl-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL", "streamable-http")# Execute workflow steps# Step 1: Get NCBI taxonomyresult_1 = await sessions["ncbi-server"].call_tool("get_taxonomy", arguments={})data_1 = parse(result_1)print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")# Step 2: Get Ensembl taxonomyresult_2 = await sessions["ensembl-server"].call_tool("get_taxonomy_id", arguments={})data_2 = parse(result_2)print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")# Step 3: Get ChEMBL organism inforesult_3 = await sessions["chembl-server"].call_tool("get_organism_by_id", arguments={})data_3 = parse(result_3)print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")# Step 4: Get genome dataset reportresult_4 = await sessions["ncbi-server"].call_tool("get_genome_dataset_report_by_taxon", 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())