list_common_attributes

Retrieve commonly used attributes for a specific dataset from BioMart databases. Streamlines dataset exploration by providing essential attributes in a CSV format for easy analysis and integration.

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
         ..."

Input Schema

TableJSON Schema

Name	Required	Description	Default
`dataset`	Yes
`mart`	Yes

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):
```

Biomart MCP