Biomart MCP

Instructions

Lists all available biomart datasets for a given mart.

Each mart contains multiple datasets. This function returns all datasets
available in the specified mart as a CSV string.

Args:
    mart (str): The mart identifier to list datasets from.
        Valid values include: ENSEMBL_MART_ENSEMBL, ENSEMBL_MART_MOUSE,
        ENSEMBL_MART_ONTOLOGY, ENSEMBL_MART_GENOMIC, ENSEMBL_MART_SNP,
        ENSEMBL_MART_FUNCGEN

Returns:
    str: CSV-formatted table of all datasets with their display names and descriptions.

Example:
    list_datasets("ENSEMBL_MART_ENSEMBL")
    >>> "name,display_name,description
         hsapiens_gene_ensembl,Human genes,Human genes (GRCh38.p13)
         mmusculus_gene_ensembl,Mouse genes,Mouse genes (GRCm39)
         ..."

Implementation Reference

• biomart-mcp.py:88-117 (handler)

  The handler function for the 'list_datasets' tool. It is decorated with @mcp.tool(), takes a 'mart' parameter, retrieves the Biomart server, lists datasets for the given mart, and returns the result as a CSV string with error handling.

  @mcp.tool()
  def list_datasets(mart: str):
      """
      Lists all available biomart datasets for a given mart.
  
      Each mart contains multiple datasets. This function returns all datasets
      available in the specified mart as a CSV string.
  
      Args:
          mart (str): The mart identifier to list datasets from.
              Valid values include: ENSEMBL_MART_ENSEMBL, ENSEMBL_MART_MOUSE,
              ENSEMBL_MART_ONTOLOGY, ENSEMBL_MART_GENOMIC, ENSEMBL_MART_SNP,
              ENSEMBL_MART_FUNCGEN
  
      Returns:
          str: CSV-formatted table of all datasets with their display names and descriptions.
  
      Example:
          list_datasets("ENSEMBL_MART_ENSEMBL")
          >>> "name,display_name,description
               hsapiens_gene_ensembl,Human genes,Human genes (GRCh38.p13)
               mmusculus_gene_ensembl,Mouse genes,Mouse genes (GRCm39)
               ..."
      """
      try:
          server = get_server()
          return server[mart].list_datasets().to_csv(index=False).replace("\r", "")
      except Exception as e:
          print(f"Error listing datasets for mart {mart}: {str(e)}", file=sys.stderr)
          return f"Error: {str(e)}"