Protein Database Crossref

---
name: protein_database_crossref
description: "Protein Cross-Database Reference - Cross-reference protein: UniProt entry, NCBI gene, Ensembl xrefs, and PDB structure search. Use this skill for proteomics tasks involving get uniprotkb entry by accession get gene metadata by gene name get xrefs symbol retrieve protein data by pdbcode. Combines 4 tools from 4 SCP server(s)."
---

# Protein Cross-Database Reference

**Discipline**: Proteomics | **Tools Used**: 4 | **Servers**: 4

## Description

Cross-reference protein: UniProt entry, NCBI gene, Ensembl xrefs, and PDB structure search.

## Tools Used

- **`get_uniprotkb_entry_by_accession`** from `uniprot-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt`
- **`get_gene_metadata_by_gene_name`** from `ncbi-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/9/Origene-NCBI`
- **`get_xrefs_symbol`** from `ensembl-server` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl`
- **`retrieve_protein_data_by_pdbcode`** from `server-2` (streamable-http) - `https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool`

## Workflow

1. Get UniProt full entry
2. Get NCBI gene data
3. Get Ensembl cross-references
4. Download PDB structure

## Test Case

### Input
```json
{
    "uniprot_accession": "P04637",
    "gene": "TP53",
    "pdb_code": "1TUP"
}
```

### Expected Steps
1. Get UniProt full entry
2. Get NCBI gene data
3. Get Ensembl cross-references
4. Download PDB structure

## Usage Example

> **Note:** Replace `<YOUR_SCP_HUB_API_KEY>` 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 mcp import ClientSession
from mcp.client.streamable_http import streamablehttp_client
from mcp.client.sse import sse_client

SERVERS = {
    "uniprot-server": "https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt",
    "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-2": "https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool"
}

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, transport

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():
    # Connect to required servers
    sessions = {}
    sessions["uniprot-server"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/10/Origene-UniProt", "streamable-http")
    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-2"], _, _ = await connect("https://scp.intern-ai.org.cn/api/v1/mcp/2/DrugSDA-Tool", "streamable-http")

    # Execute workflow steps
    # Step 1: Get UniProt full entry
    result_1 = await sessions["uniprot-server"].call_tool("get_uniprotkb_entry_by_accession", arguments={})
    data_1 = parse(result_1)
    print(f"Step 1 result: {json.dumps(data_1, indent=2, ensure_ascii=False)[:500]}")

    # Step 2: Get NCBI gene data
    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 Ensembl cross-references
    result_3 = await sessions["ensembl-server"].call_tool("get_xrefs_symbol", arguments={})
    data_3 = parse(result_3)
    print(f"Step 3 result: {json.dumps(data_3, indent=2, ensure_ascii=False)[:500]}")

    # Step 4: Download PDB structure
    result_4 = await sessions["server-2"].call_tool("retrieve_protein_data_by_pdbcode", 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())
```