biomarker_discovery

# Biomarker Discovery Pipeline

**Discipline**: Precision Medicine | **Tools Used**: 4 | **Servers**: 4

## Description

Discover biomarkers: TCGA differential expression, NCBI gene data, OpenTargets associations, and clinical relevance.

## Tools Used

- **`tcga_differential_expression_analysis`** from `tcga-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA`
- **`get_gene_metadata_by_gene_name`** from `ncbi-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI`
- **`get_associated_targets_by_disease_efoId`** from `opentargets-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets`
- **`clinvar_search`** from `search-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search`

## Workflow

1. Run TCGA differential expression
2. Get gene metadata
3. Get OpenTargets associations
4. Search ClinVar variants

## Test Case

### Input
```json
{
    "query": "biomarkers for breast cancer",
    "gene": "BRCA1",
    "disease_efo": "EFO_0000305"
}
```

### Expected Steps
1. Run TCGA differential expression
2. Get gene metadata
3. Get OpenTargets associations
4. Search ClinVar variants

## 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 = {
    "tcga-server": "https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA",
    "ncbi-server": "https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI",
    "opentargets-server": "https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets",
    "search-server": "https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search"
}

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["tcga-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/11/Origene-TCGA", stack)
        sessions["ncbi-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI", stack)
        sessions["opentargets-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/15/Origene-OpenTargets", stack)
        sessions["search-server"] = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/7/Origene-Search", stack)

        # Execute workflow steps
        # Step 1: Run TCGA differential expression
        result_1 = await sessions["tcga-server"].call_tool("tcga_differential_expression_analysis", arguments={})
        data_1 = parse(result_1)
        print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

        # Step 2: Get gene metadata
        result_2 = await sessions["ncbi-server"].call_tool("get_gene_metadata_by_gene_name", arguments={})
        data_2 = parse(result_2)
        print(f"Step 2 result: {json.dumps(data_2, indent=2, ensure_ascii=False)[:500]}")

        # Step 3: Get OpenTargets associations
        result_3 = await sessions["opentargets-server"].call_tool("get_associated_targets_by_disease_efoId", 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 variants
        result_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]}")

        # Cleanup
        print("Workflow complete!")

if __name__ == "__main__":
    asyncio.run(main())
```