NCBI Gene MCP Server

Instructions

Implementation Reference

• ncbi_gene_mcp_client/bridge.py:125-172 (handler)

  Core implementation of fetch_gene_info: queries NCBI Entrez esummary API, parses response, constructs GeneInfo object.

  def fetch_gene_info(self, gene_id: str) -> GeneInfo:
      """
      Fetch detailed information for a specific gene.
      
      Args:
          gene_id: NCBI Gene ID
          
      Returns:
          GeneInfo object with gene details
      """
      params = {
          "db": "gene",
          "id": gene_id
      }
      
      response = self._make_request("esummary", params)
      
      result = response.get("result", {})
      gene_data = result.get(gene_id)
      
      if not gene_data:
          raise Exception(f"No data found for gene ID: {gene_id}")
      
      # Extract organism information
      organism = gene_data.get("organism", {})
      organism_name = organism.get("scientificname", "Unknown") if isinstance(organism, dict) else str(organism)
      
      # Extract other aliases
      other_aliases = []
      if "otheraliases" in gene_data:
          aliases = gene_data["otheraliases"]
          if isinstance(aliases, str):
              other_aliases = [alias.strip() for alias in aliases.split(",")]
          elif isinstance(aliases, list):
              other_aliases = aliases
      
      return GeneInfo(
          gene_id=gene_id,
          name=gene_data.get("name", ""),
          description=gene_data.get("description", ""),
          organism=organism_name,
          chromosome=gene_data.get("chromosome"),
          map_location=gene_data.get("maplocation"),
          gene_type=gene_data.get("geneticsource"),
          other_aliases=other_aliases if other_aliases else None,
          summary=gene_data.get("summary")
      )

• ncbi_gene_mcp_client/mcp_server.py:89-102 (registration)

  MCP tool registration: defines name, description, and input schema for fetch_gene_info in tools/list response.

  {
      "name": "fetch_gene_info",
      "description": "Fetch detailed information for a specific gene ID",
      "inputSchema": {
          "type": "object",
          "properties": {
              "gene_id": {
                  "type": "string",
                  "description": "NCBI Gene ID (e.g., '672' for BRCA1)"
              }
          },
          "required": ["gene_id"]
      }
  },

• ncbi_gene_mcp_client/mcp_server.py:159-171 (handler)

  MCP server dispatch handler for fetch_gene_info tool call: validates input, calls bridge, formats JSON response.

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