NCBI Gene MCP Server

Instructions

Implementation Reference

• ncbi_gene_mcp_client/bridge.py:98-124 (handler)

  Core implementation of the search_genes tool using NCBI Entrez esearch API to search the gene database.

  def search_genes(self, query: str, max_results: int = 20) -> SearchResult:
      """
      Search for genes using NCBI Entrez.
      
      Args:
          query: Search query (gene name, symbol, etc.)
          max_results: Maximum number of results to return
          
      Returns:
          SearchResult object containing IDs and metadata
      """
      params = {
          "db": "gene",
          "term": query,
          "retmax": max_results
      }
      
      response = self._make_request("esearch", params)
      
      esearch_result = response.get("esearchresult", {})
      
      return SearchResult(
          count=int(esearch_result.get("count", 0)),
          ids=esearch_result.get("idlist", []),
          query_translation=esearch_result.get("querytranslation")
      )

• ncbi_gene_mcp_client/mcp_server.py:71-88 (registration)

  Registration of the search_genes tool in the MCP server's tools/list, defining name, description, and input schema.

      "name": "search_genes",
      "description": "Search for genes in NCBI database using a query",
      "inputSchema": {
          "type": "object",
          "properties": {
              "query": {
                  "type": "string",
                  "description": "Search query (gene name, symbol, etc.)"
              },
              "max_results": {
                  "type": "integer",
                  "description": "Maximum number of results to return (default: 20)",
                  "default": 20
              }
          },
          "required": ["query"]
      }
  },

• ncbi_gene_mcp_client/mcp_server.py:145-157 (handler)

  MCP server handler for tools/call requests to search_genes, extracting parameters and calling the bridge implementation.

  if name == "search_genes":
      query = arguments.get("query")
      max_results = arguments.get("max_results", 20)
      if not query:
          raise ValueError("query is required")
      
      result = self.bridge.search_genes(query, max_results)
      self.send_response({
          "content": [{
              "type": "text", 
              "text": f"Found {result.count} genes matching '{query}':\n\nGene IDs: {', '.join(result.ids[:10])}\n\nQuery translation: {result.query_translation or 'N/A'}"
          }]
      })

• ncbi_gene_mcp_client/models.py:33-39 (schema)

  Pydantic model SearchResult used as return type for search_genes, defining structure of search results.

  class SearchResult(BaseModel):
      """Model for search results from NCBI Entrez."""
      
      count: int = Field(description="Total number of results")
      ids: List[str] = Field(description="List of IDs found")
      query_translation: Optional[str] = Field(default=None, description="Translated query")

• ncbi_gene_mcp_client/mcp_server.py:73-86 (schema)

  Input schema definition for search_genes tool in MCP registration.

  "inputSchema": {
      "type": "object",
      "properties": {
          "query": {
              "type": "string",
              "description": "Search query (gene name, symbol, etc.)"
          },
          "max_results": {
              "type": "integer",
              "description": "Maximum number of results to return (default: 20)",
              "default": 20
          }
      },
      "required": ["query"]