Skip to content

Mondo mapping

map_disease_id(disease_identifier, mondo_mapping_table)

Map a disease identifier to MONDO ID using the Mondo SSSOM mapping. Args: disease_identifier (str): The disease identifier to map to MONDO. mondo_mapping_table (pl.DataFrame): The Mondo SSSOM table. Returns: str: The MONDO ID.

Source code in src/pheval/post_processing/mondo_mapping.py 
23
24
25
26
27
28
29
30
31
32
33
34
35
def map_disease_id(disease_identifier: str, mondo_mapping_table: pl.DataFrame) -> str:
    """
    Map a disease identifier to MONDO ID using the Mondo SSSOM mapping.
    Args:
        disease_identifier (str): The disease identifier to map to MONDO.
        mondo_mapping_table (pl.DataFrame): The Mondo SSSOM table.
    Returns:
        str: The MONDO ID.
    """
    mapped_identifier = mondo_mapping_table.filter(pl.col("object_id") == disease_identifier)
    if mapped_identifier.height > 0:
        return mapped_identifier["subject_id"].item()
    return disease_identifier

parse_mondo_mapping_table()

Parse the Mondo SSSOM table. Returns: pl.DataFrame: Mondo SSSOM table.

Source code in src/pheval/post_processing/mondo_mapping.py 
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
def parse_mondo_mapping_table() -> pl.DataFrame:
    """
    Parse the Mondo SSSOM table.
    Returns:
        pl.DataFrame: Mondo SSSOM table.
    """
    df = pl.read_csv(
        Path(__file__).parent.parent / "resources" / "mondo.sssom.tsv",
        separator="\t",
        comment_prefix="#",
    )
    orphanet_rows = df.filter(pl.col("object_id").str.starts_with("Orphanet:"))
    orpha_rows = orphanet_rows.with_columns(pl.col("object_id").str.replace("^Orphanet:", "ORPHA:").alias("object_id"))

    return pl.concat([df, orpha_rows], how="vertical")