Biomart MCP

Instructions

Lists commonly used attributes available for a given dataset.

This function returns only the most frequently used attributes (defined in COMMON_ATTRIBUTES)
to avoid overwhelming the model with too many options. For a complete list,
use list_all_attributes.

Args:
    mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL")
    dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl")

Returns:
    str: CSV-formatted table of common attributes with their display names and descriptions.

Example:
    list_common_attributes("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl")
    >>> "name,display_name,description
         ensembl_gene_id,Gene stable ID,Ensembl stable ID for the gene
         external_gene_name,Gene name,The gene name
         ..."

Implementation Reference

• biomart-mcp.py:120-146 (handler)

  The handler function for the 'list_common_attributes' tool. It connects to the Biomart server, lists all attributes for the dataset, filters to common ones defined in COMMON_ATTRIBUTES, and returns as CSV.

  @mcp.tool()
  def list_common_attributes(mart: str, dataset: str):
      """
      Lists commonly used attributes available for a given dataset.
  
      This function returns only the most frequently used attributes (defined in COMMON_ATTRIBUTES)
      to avoid overwhelming the model with too many options. For a complete list,
      use list_all_attributes.
  
      Args:
          mart (str): The mart identifier (e.g., "ENSEMBL_MART_ENSEMBL")
          dataset (str): The dataset identifier (e.g., "hsapiens_gene_ensembl")
  
      Returns:
          str: CSV-formatted table of common attributes with their display names and descriptions.
  
      Example:
          list_common_attributes("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl")
          >>> "name,display_name,description
               ensembl_gene_id,Gene stable ID,Ensembl stable ID for the gene
               external_gene_name,Gene name,The gene name
               ..."
      """
      server = pybiomart.Server(host=DEFAULT_HOST)
      df = server[mart][dataset].list_attributes()
      df = df[df["name"].isin(COMMON_ATTRIBUTES)]
      return df.to_csv(index=False).replace("\r", "")

• biomart-mcp.py:120-120 (registration)

  The @mcp.tool() decorator registers the list_common_attributes function as an MCP tool.

  @mcp.tool()

• biomart-mcp.py:28-47 (helper)

  Predefined list of common attributes used by the list_common_attributes handler to filter the full attribute list.

  COMMON_ATTRIBUTES = [
      "ensembl_gene_id",
      "external_gene_name",
      "hgnc_symbol",
      "hgnc_id",
      "gene_biotype",
      "ensembl_transcript_id",
      "ensembl_peptide_id",
      "ensembl_exon_id",
      "description",
      "chromosome_name",
      "start_position",
      "end_position",
      "strand",
      "band",
      "transcript_start",
      "transcript_end",
      "transcription_start_site",
      "transcript_length",
  ]

• biomart-mcp.py:121-121 (schema)

  Function signature defining input parameters with type annotations, which serves as the input schema for the tool.

  def list_common_attributes(mart: str, dataset: str):