pypath.inputs.oma.oma_table

pypath.inputs.oma.oma_table(organism_a: str | int = 'human', organism_b: str | int = 'mouse', id_type: str | None = None, rel_type: set[Literal['1:1', '1:n', 'm:1', 'm:n']] | None = None, score: float = None, return_df: bool = False) → dict[str[set[str]]] | pd.DataFrame

Translation table of orthologous gene pairs between two organisms from the OMA (Orthologous Matrix) database (https://omabrowser.org/oma/home/).

Parameters:

• organism_a – Name or NCBI Taxonomy ID of the first organism.

• organism_b – Name or NCBI Taxonomy ID of the second organism.

• id_type – OMA by default uses UniProt entry IDs and sometimes other identifiers for genes. Set this parameter to control which ID type all the identifiers are to be mapped to.

• rel_type – Restrict relations to certain types.

• score – Lower threshold for similarity metric.

• return_df – If True, returns a data frame instead of a list of tuples.

Returns:

A dict with source organism identifiers as keys and sets of target organism identifiers as values; or a two column data frame with source organism-target organism identifier pairs.