NCBI Gene MCP Server

Instructions

Implementation Reference

• ncbi_gene_mcp_client/bridge.py:173-202 (handler)

  Core handler function that performs the NCBI esummary API call for protein database and constructs ProteinInfo object.

  def fetch_protein_info(self, protein_id: str) -> ProteinInfo:
      """
      Fetch detailed information for a specific protein.
      
      Args:
          protein_id: NCBI Protein ID
          
      Returns:
          ProteinInfo object with protein details
      """
      params = {
          "db": "protein",
          "id": protein_id
      }
      
      response = self._make_request("esummary", params)
      
      result = response.get("result", {})
      protein_data = result.get(protein_id)
      
      if not protein_data:
          raise Exception(f"No data found for protein ID: {protein_id}")
      
      return ProteinInfo(
          protein_id=protein_id,
          title=protein_data.get("title", ""),
          organism=protein_data.get("organism", ""),
          length=protein_data.get("slen"),
          mol_type=protein_data.get("moltype")
      )

• ncbi_gene_mcp_client/models.py:23-31 (schema)

  Pydantic model defining the structure and validation for the protein information output.

  class ProteinInfo(BaseModel):
      """Model for protein information from NCBI Entrez."""
      
      protein_id: str = Field(description="NCBI Protein ID")
      title: str = Field(description="Protein title")
      organism: str = Field(description="Organism scientific name")
      length: Optional[int] = Field(default=None, description="Protein sequence length")
      mol_type: Optional[str] = Field(default=None, description="Molecule type")

• ncbi_gene_mcp_client/mcp_server.py:103-116 (registration)

  MCP tool registration entry providing the tool name, description, and input schema.

  {
      "name": "fetch_protein_info",
      "description": "Fetch detailed information for a specific protein ID",
      "inputSchema": {
          "type": "object",
          "properties": {
              "protein_id": {
                  "type": "string",
                  "description": "NCBI Protein ID"
              }
          },
          "required": ["protein_id"]
      }
  },

• ncbi_gene_mcp_client/mcp_server.py:173-185 (handler)

  MCP server dispatch handler that extracts arguments, calls bridge, serializes to JSON, and sends response.

  elif name == "fetch_protein_info":
      protein_id = arguments.get("protein_id")
      if not protein_id:
          raise ValueError("protein_id is required")
      
      result = self.bridge.fetch_protein_info(protein_id)
      protein_json = result.model_dump_json(indent=2)
      self.send_response({
          "content": [{
              "type": "text", 
              "text": f"Protein Information for ID {protein_id}:\n\n{protein_json}"
          }]
      })

• ncbi_gene_mcp_client/mcp_server.py:106-115 (schema)

  Input schema definition for the fetch_protein_info tool in MCP registration.

  "inputSchema": {
      "type": "object",
      "properties": {
          "protein_id": {
              "type": "string",
              "description": "NCBI Protein ID"
          }
      },
      "required": ["protein_id"]
  }