BioMCP

Instructions

⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal!

Provides real-time gene annotations including:
- Official gene name and symbol
- Gene summary/description
- Aliases and alternative names
- Gene type (protein-coding, etc.)
- Links to external databases

This tool fetches CURRENT gene information from MyGene.info, ensuring
you always have the latest annotations and nomenclature.

Example usage:
- Get information about TP53 tumor suppressor
- Look up BRAF kinase gene details
- Find the official name for a gene by its alias

Note: For genetic variants, use variant_searcher. For articles about genes, use article_searcher.

Implementation Reference

• src/biomcp/individual_tools.py:718-755 (handler)

  The primary handler function for the 'gene_getter' MCP tool. Registered via @mcp_app.tool() decorator. Includes schema via Annotated Field and executes by delegating to _gene_details.

  @mcp_app.tool()
  @track_performance("biomcp.gene_getter")
  async def gene_getter(
      gene_id_or_symbol: Annotated[
          str,
          Field(
              description="Gene symbol (e.g., 'TP53', 'BRAF') or Entrez ID (e.g., '7157')"
          ),
      ],
  ) -> str:
      """Get detailed gene information from MyGene.info.
  
      ⚠️ PREREQUISITE: Use the 'think' tool FIRST to understand your research goal!
  
      Provides real-time gene annotations including:
      - Official gene name and symbol
      - Gene summary/description
      - Aliases and alternative names
      - Gene type (protein-coding, etc.)
      - Links to external databases
  
      This tool fetches CURRENT gene information from MyGene.info, ensuring
      you always have the latest annotations and nomenclature.
  
      Example usage:
      - Get information about TP53 tumor suppressor
      - Look up BRAF kinase gene details
      - Find the official name for a gene by its alias
  
      Note: For genetic variants, use variant_searcher. For articles about genes, use article_searcher.
      """
      return await _gene_details(
          call_benefit="Get up-to-date gene annotations and information",
          gene_id_or_symbol=gene_id_or_symbol,
      )
  
  
  # Disease Tools

• src/biomcp/genes/getter.py:15-79 (helper)

  Core helper function implementing the gene fetching logic from MyGene.info via BioThingsClient, formatting as markdown or JSON.

  async def get_gene(
      gene_id_or_symbol: str,
      output_json: bool = False,
  ) -> str:
      """
      Get gene information from MyGene.info.
  
      Args:
          gene_id_or_symbol: Gene ID (Entrez, Ensembl) or symbol (e.g., "TP53", "7157")
          output_json: Return as JSON instead of markdown
  
      Returns:
          Gene information as markdown or JSON string
      """
      client = BioThingsClient()
  
      try:
          gene_info = await client.get_gene_info(gene_id_or_symbol)
  
          if not gene_info:
              error_data = {
                  "error": f"Gene '{gene_id_or_symbol}' not found",
                  "suggestion": "Please check the gene symbol or ID",
              }
              return (
                  json.dumps(error_data, indent=2)
                  if output_json
                  else to_markdown([error_data])
              )
  
          # Convert to dict for rendering
          result = gene_info.model_dump(exclude_none=True)
  
          # Add helpful links
          if gene_info.entrezgene:
              result["_links"] = {
                  "NCBI Gene": f"https://www.ncbi.nlm.nih.gov/gene/{gene_info.entrezgene}",
                  "PubMed": f"https://pubmed.ncbi.nlm.nih.gov/?term={gene_info.symbol}",
              }
  
          # Format aliases nicely
          if gene_info.alias:
              result["alias"] = ", ".join(
                  gene_info.alias[:10]
              )  # Limit to first 10
              if len(gene_info.alias) > 10:
                  result["alias"] += f" (and {len(gene_info.alias) - 10} more)"
  
          if output_json:
              return json.dumps(result, indent=2)
          else:
              return to_markdown([result])
  
      except Exception as e:
          logger.error(f"Error fetching gene info for {gene_id_or_symbol}: {e}")
          error_data = {
              "error": "Failed to retrieve gene information",
              "details": str(e),
          }
          return (
              json.dumps(error_data, indent=2)
              if output_json
              else to_markdown([error_data])
          )

• src/biomcp/genes/getter.py:81-111 (helper)

  Intermediate helper wrapper called by the handler, delegates to get_gene with markdown output.

  async def _gene_details(
      call_benefit: Annotated[
          str,
          "Define and summarize why this function is being called and the intended benefit",
      ],
      gene_id_or_symbol: Annotated[
          str,
          Field(description="Gene symbol (e.g., TP53, BRAF) or ID (e.g., 7157)"),
      ],
  ) -> str:
      """
      Retrieves detailed information for a single gene from MyGene.info.
  
      This tool provides real-time gene annotations including:
      - Official gene name and symbol
      - Gene summary/description
      - Aliases and alternative names
      - Gene type (protein-coding, etc.)
      - Links to external databases
  
      Parameters:
      - call_benefit: Define why this function is being called
      - gene_id_or_symbol: Gene symbol (e.g., "TP53") or Entrez ID (e.g., "7157")
  
      Process: Queries MyGene.info API for up-to-date gene annotations
      Output: Markdown formatted gene information with description and metadata
  
      Note: For variant information, use variant_searcher. For articles about genes, use article_searcher.
      """
      return await get_gene(gene_id_or_symbol, output_json=False)

• src/biomcp/individual_tools.py:718-719 (registration)

  Registration decorators for the gene_getter tool in the MCP app.

  @mcp_app.tool()
  @track_performance("biomcp.gene_getter")

• src/biomcp/individual_tools.py:721-727 (schema)

  Pydantic schema definition for the tool input parameter via Annotated Field.

      gene_id_or_symbol: Annotated[
          str,
          Field(
              description="Gene symbol (e.g., 'TP53', 'BRAF') or Entrez ID (e.g., '7157')"
          ),
      ],
  ) -> str: